Docswiki - User contributions [en]

Decoding heat capacity curves

2022-11-15T13:24:23Z

Nn320:

This is a short introduction on how to analyse and decode heat capacity curve features (D.J. Wales ''Phys. Rev. E'' '''95''', 030105(R), 2017).

After creating your data base of stationary points the analysis of the heat capacity curve is a common next step. To locate the minima contributing to the changes in occupational probability at specific temperatures (i.e. at features in the heat capacity) the following steps should be followed.

First of all you will need to compile the analysis script. It is part of the svn at '''~/softwarewales/UTILS/GMIN/Cv.HSA.f90'''

Then two additional input files are needed:

<pre>
0.10 2.0 1901 3168 27125
</pre>
'''Cv.data'''

The entries are the lowest and highest temperature for the heat capacity calculations, the number of data points calculated with these limits, the number of degrees of freedom, and the number of minima.

<pre>
1.3176
0.99
</pre>
'''Tanal'''

Here the first entry is the temperature in the native units of your system (e.g. for AMBER it would be in kcal/mol). The second line quantifies how much of the changes in occupational probability should be accounted for (here it is that all changes sum to 99% of the total change).

Running the script may take some time. At the end ths script should print the following line:

<pre>
For disconnectionDPS use line TRMIN 2 27125 min.minus min.plus and
CHOOSECOLOURS in the dinfo file
</pre>

Add these two lines to your dinfo file and the contributing minima will be highlighted. A common problem is that the coloured branches are covered by black branches. To get around this problem either change the ps file to move all coloured branches to the end, so they are drawn on top, or increase the line width for the coloured branches.

Preparing input files for a peptide using AMBER

2022-11-15T12:32:56Z

Nn320: /* Step 7: Creating topology file for modified force field ff99IDPs */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Download and install AMBER===

Follow the installation steps given in AMBER manual after downloading AMBER 14. [For group members: amber14 directory is present on nest in /home/nn320/amber14].
You can have AMBER in your path by having something similar to this in ~/.bashrc.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crsid/amber14/lib
export PATH
</pre>
Then from the command line run, <pre>source ~/.bashrc</pre>
Now you can run tleap from anywhere on your system.

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
The following is an example of leap.in for modelling a capped peptide using FF99SBildn AMBER force field.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This generates initial topology (prmtop), coordinates (inpcrd), and pdb files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper initial geometry.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct. They are correct for FF99SBildn force field used here.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and md_min.in file.
md_min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i md_min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them. If you get the same energy for all such structures it means that the topology file is symmetrised properly.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD_CMAP.py -p old_symmetrised_coords.prmtop -c ff99IDPs.para -o coords.prmtop -s</pre>
Here, old_symmetrised_coords.prmtop represents the symmetrised prmtop and coords.prmtop
is the topology file for using with GMIN, OPTIM and PATHSAMPLE.
These files ADD_CMAP.py and ff99IDPs.para can be found on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.
Both were checked and they are working for FF99IDPs force field.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2022-11-15T12:27:29Z

Nn320: /* Step 4: Symmetrise the topology file so obtained */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Download and install AMBER===

Follow the installation steps given in AMBER manual after downloading AMBER 14. [For group members: amber14 directory is present on nest in /home/nn320/amber14].
You can have AMBER in your path by having something similar to this in ~/.bashrc.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crsid/amber14/lib
export PATH
</pre>
Then from the command line run, <pre>source ~/.bashrc</pre>
Now you can run tleap from anywhere on your system.

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
The following is an example of leap.in for modelling a capped peptide using FF99SBildn AMBER force field.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This generates initial topology (prmtop), coordinates (inpcrd), and pdb files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper initial geometry.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct. They are correct for FF99SBildn force field used here.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and md_min.in file.
md_min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i md_min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them. If you get the same energy for all such structures it means that the topology file is symmetrised properly.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2022-11-15T12:25:36Z

Nn320: /* Step 3: Minimising the structure using sander */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Download and install AMBER===

Follow the installation steps given in AMBER manual after downloading AMBER 14. [For group members: amber14 directory is present on nest in /home/nn320/amber14].
You can have AMBER in your path by having something similar to this in ~/.bashrc.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crsid/amber14/lib
export PATH
</pre>
Then from the command line run, <pre>source ~/.bashrc</pre>
Now you can run tleap from anywhere on your system.

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
The following is an example of leap.in for modelling a capped peptide using FF99SBildn AMBER force field.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This generates initial topology (prmtop), coordinates (inpcrd), and pdb files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper initial geometry.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct. They are correct for FF99SBildn force field used here.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and md_min.in file.
md_min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i md_min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2022-11-15T12:23:39Z

Nn320: /* Step 1: Make topology and coordinates file using tleap in AMBER */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Download and install AMBER===

Follow the installation steps given in AMBER manual after downloading AMBER 14. [For group members: amber14 directory is present on nest in /home/nn320/amber14].
You can have AMBER in your path by having something similar to this in ~/.bashrc.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crsid/amber14/lib
export PATH
</pre>
Then from the command line run, <pre>source ~/.bashrc</pre>
Now you can run tleap from anywhere on your system.

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
The following is an example of leap.in for modelling a capped peptide using FF99SBildn AMBER force field.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This generates initial topology (prmtop), coordinates (inpcrd), and pdb files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper initial geometry.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct. They are correct for FF99SBildn force field used here.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2022-11-15T12:23:07Z

Nn320: /* Step 1: Make topology and coordinates file using tleap in AMBER */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Download and install AMBER===

Follow the installation steps given in AMBER manual after downloading AMBER 14. [For group members: amber14 directory is present on nest in /home/nn320/amber14].
You can have AMBER in your path by having something similar to this in ~/.bashrc.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crsid/amber14/lib
export PATH
</pre>
Then from the command line run, <pre>source ~/.bashrc</pre>
Now you can run tleap from anywhere on your system.

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
The following is an example of leap.in for modelling a capped peptide using FF99SBildn AMBER force field.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This generates initial topology (prmtop), coordinates (inpcrd), and pdb files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper initial geometry.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2022-11-15T12:19:12Z

Nn320: /* Step 0: Download and install AMBER */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Download and install AMBER===

Follow the installation steps given in AMBER manual after downloading AMBER 14. [For group members: amber14 directory is present on nest in /home/nn320/amber14].
You can have AMBER in your path by having something similar to this in ~/.bashrc.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crsid/amber14/lib
export PATH
</pre>
Then from the command line run, <pre>source ~/.bashrc</pre>
Now you can run tleap from anywhere on your system.

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2022-11-15T12:18:26Z

Nn320: /* Step 0: Have amber on your system */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Download and install AMBER===

Follow the installation steps given in AMBER manual after downloading AMBER 14. [For group members: amber14 directory is present on nest in /home/nn320/amber14].
You can have AMBER in your path by having something similar to this in ~/.bashrc.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crsid/amber14/lib
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system.

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Adding several minima obtained using GMIN (maybe using BHPT) to min.data

2021-10-28T10:20:31Z

Nn320: Created page with "For biomolecules, if you know the global minimum, then try to save (using SAVE keyword in GMIN) minima within 20 kcal/mol of global minimum. The minima are saved in xyz format..."

For biomolecules, if you know the global minimum, then try to save (using SAVE keyword in GMIN) minima within 20 kcal/mol of global minimum. The minima are saved in xyz format in “lowest” file. The lowest file can then be renamed as lowest.xyz. In pathdata, use the keyword “ADDMINXYZ lowest.xyz” to create various min.data.info.n files. Concatenate all the min.data.info.n files into one file called allmin.data.info and run PATHSAMPLE again using the keyword “ADDMIN allmin.data.info”.
Please note that if you are not using the keyword “CPUS 1” in pathdata, then the number of CYCLES in pathdata should be such that number of minima to be added = CYCLES * number of cores specified in submission script. Usually, we give some extra CYCLES just to be on the safe side.
While running PATHSAMPLE with “ADDMINXYZ lowest.xyz” keyword, make sure that odata.addminxyz has the keywords ENDNUMHESS and DUMPDATA specified in it. You should not use NOFRQS as frequencies will not be calculated in this case. Note that frequencies are required if you want to calculate thermodynamic and kinetic properties. Also, make sure your odata.addminxyz just has the minimisation keywords specified and you are not trying to run a double ended search.
An example odata.addminxyz file when using AMBER potential is
<pre>
DEBUG
REOPTIMISEENDPOINTS
BFGSMIN 1.0D-6
NOCISTRANS
LPERMDIST 11 0.5 5.0 0.06
NOHESS ENDNUMHESS
GEOMDIFFTOL 0.3
EDIFFTOL 1.0D-4
DUMPDATA
AMBER12 start
</pre>

Comprehensive Contents Page

2021-10-28T10:17:15Z

Nn320: /* PATHSAMPLE */

This page is designed to organise all of the pages on this wiki, as well as provide other useful links. Note that some pages may appear under more than one heading.

== Getting Started ==
[[Wales Group]] provides good step-by-step instructions. Relevant pages are:

=== Acquiring and compiling the group software ===
* [[SVN setup]]
* [[Git Workflow]]
* [[Wales Group Version control]] - to keep the code standardised.
* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.
* [[Compiling Wales Group codes using cmake]] - CMake (Cross-platform Make) allows us to compile and test the group codebase regardless of platform. This page provides crucial information how to compile using cmake.
* [[ElaborateDiff]]

=== Maintaining code health ===
* [[Jenkins CI]] - explains Jenkins, which we use to download our code and compile each of our targets with each of the compilers every night.
* https://wales-jenkins.ch.cam.ac.uk/ - log for our Jenkins tests.
* [[Branching and Merging]]
* [[Cmake interface building]]
* [[Installing python modules]]
* [[Revamping the modules system]]

=== Collaborators without access to the SVN repository ===
For licensing reasons, some code cannot be included in the Wales Group public tarball.
* http://www-wales.ch.cam.ac.uk/svn.tar.bz2 - Wales group public tarball. Includes [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]].
If a collaborator has a [[CHARMM]] or [[AMBER]] licence, we do maintain separate tarballs which include the [[CHARMM]], [[AMBER]] and [[CHARMM]]+[[AMBER]] source and interfaces. These are not linked anywhere on the website and require a username ('''wales''') and password ('''group''') to download:

* [http://www-wales.ch.cam.ac.uk/CHARMM/svn.CHARMM.tar.bz2 CHARMM]
* [http://www-wales.ch.cam.ac.uk/AMBER/svn.AMBER.tar.bz2 AMBER]
* [http://www-wales.ch.cam.ac.uk/both/svn.both.tar.bz2 AMBER+CHARMM]

=== Running on Windows ===
Not particularly recommended.
* [[Running Wales Group software on Windows 7]]

== Wales Group Programs ==

=== Programs ===
* [[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
* [[OPTIM]]: A program for optimizing geometries and calculating reaction pathways.
* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.
* [[DISCOTRESS]]: A program to perform detailed quantitative analysis of a kinetic network (stationary point database)

=== Curated Examples ===
* https://github.com/wales-group/examples - set of tutorials detailing how to use GMIN, OPTIM and PATHSAMPLE. Essential for beginners.
* http://www-wales.ch.cam.ac.uk/VM/Wales_Group_VM.ova - Pre-prepared teaching virtual machine. This contains the code and examples.
* https://www.virtualbox.org/wiki/Downloads - This is required if using the VM above.
* https://github.com/wales-group/examples.git - Alternatively, you can run the examples on your own machine. To get hold of the relevant files:
<pre>
git clone https://github.com/wales-group/examples.git
</pre>

== Useful Notes on Wales Group Programs and Subroutines ==
=== [[GMIN]] ===
* [[Adding a model to GMIN]] - rough outline of the subroutines that need to be changed to add a new model to GMIN
* [[Compiling Wales Group codes using cmake | Compiling GMIN using cmake ]]
* [[Selecting search parameters for GMIN]]
* [[Global optimization of biomolecules using CHARMM]]
* [[Global optimization of biomolecules using AMBER9]]
* [[Global optimization of biomolecules using AMBER9 with Structural Restraints]]
* [[Calculating binding free energy using the FSA method]]
* [[Restarting a GMIN run from a dump file]]
* [[Using the implicit membrane model IMM1]]
* [[Running a Go model with the AMHGMIN]]
* [[Running a G\=o model with the AMHGMIN]]
* [[Ligand binding-mode searches with HBONDMATRIX]]
* [[Compiling and using GMIN with QUIP]]
* [[Using GMIN and OPTIM with GPUs]]
* [[Using GMIN to generate endpoints]]
* [[Using GMIN to generate endpoints (CHARMM)]]
* [[Generating a GMIN Eclipse project]]
* [[Mutational BH steps]]
* [[Biomolecules in the energy landscape framework]]
* [[DMAGMIN setup]]
* [[Keywords]]
* [[PYGMIN & DMACRYS]]
* [[Rotamer moves in AMBER]]
* [[Python interface for GMIN/OPTIM]]

==== Scripts ====
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining

==== Useful info for coding GMIN ====
* [[Program flow]] - contains information about what the various files in GMIN do and what order they're called.
* [[amberinterface]]

==== Projects ====
* [[GMIN MOVES module]]
* [[GMIN SANITY module]]
* [[GMIN TESTS module]]
* [[CAMSHIFT]]

=== [[OPTIM]] ===
* [[Adding a model to OPTIM]] - rough outline of the subrounties that need to be changed to add a new model to OPTIM
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[visualising normal modes using VMD and OPTIM]]
* [[Compiling Wales Group codes using cmake | Compiling OPTIM using cmake ]]
* [[OPTIM/Q-Chem Tutorial]]
* [[OPTIM and PY ellipsoids tutorial]]
* [[OPTIM output files]]
* [[Minimizing a structure using OPTIM and AMBER9]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Creating movies (.mpg) of paths using OPTIM]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Debugging odd transition states in OPTIM]]
* [[Connecting two minima with a pathway]] - step by step
* [[Compiling and using OPTIM with QUIP]]
* [[Running an Gaussian03 interfaced OPTIM job]]
* [[The effect of calculating less than the maximum number of eigenvalues using ENDHESS n]]
* [[Biomolecules in the energy landscape framework]]
* [[BLJ60 example setup]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Python interface for GMIN/OPTIM]]
* [[Thomson problem in OPTIM]]
* [[Instanton tunneling and classical rate calculations with OPTIM]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[common setup problem : No Frequency Warning]]

=== [[PATHSAMPLE]] ===
* [[Adding a model to PATHSAMPLE]] - rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[Compiling Wales Group codes using cmake | Compiling PATHSAMPLE using cmake ]]
* [[IMPORTANT: Using PATHSAMPLE safely on sinister]]
* [[Adding a model for PATHSAMPLE]]
* [[List of output files for PATHSAMPLE]]
* [[Using BHINTERP to find minima between two end points]]
* [[Finding an initial path between two end points (minima)]]
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[Optimising a path]]
* [[Fine tuning UNTRAP]] - ensuring that it picks sensible minima
* [[Calculating rate constants (GT and fastest path)]]
* [[Calculating rate constants (SGT, DGT, and SDGT)]]
* [[Identifying the k fastest paths between endpoints using KSHORTESTPATHS]]
* [[Removing minima and transition states from the database]]
* [[Relaxing existing minima with new potential and creating new database]]
* [[Relaxing existing transition states with new potential and creating new database]]
* [[If things go wrong...]]
* [[If you lost file min.data, but still you have points.min]]
* [[path.info file is not read, causes PATHSAMPLE to die]]
* [[BLJ60 example setup]]
* [[When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path]]
* [[Biomolecules in PATHSAMPLE]]
* [[Biomolecules in the energy landscape framework]]
* [[Adding several minima obtained using GMIN (maybe using BHPT) to min.data]]
* [[Expanding the kinetic transition network with PATHSAMPLE]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths]]
* [[Pathsampling short paths (CHARMM)]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[Connecting Sub-databases]]
* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
* [[STARTING INITIAL PATH JOBS WITH PATHSAMPLE]]: How to start initial path jobs with PATHSAMPLE if no min.data or path.info files are present.

=== [[Notes on MINPERMDIST | MINPERMDIST]] ===

=== [[Quasi-continuous interpolation for biomolecules | QCI]] ===

=== [[DISCOTRESS | Detailed kinetic network analysis with DISCOTRESS]] ===

== Non-Group Software ==

=== [[AMBER]] ===
Molecular dynamics simulation program and associated force fields.
* [http://ambermd.org/ AMBER]
* [http://ambermd.org/tutorials/ AMBER tutorials] - recommended reading for '''ANYONE''' using AMBER!
* [[Notes on AMBER 12 interface]]
* [[Using AMBER 14 on the GPU and compute clusters]]
* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
* [[Generating parameters using RESP charges from GAMESS-US]]
* [[Simple scripts for LEaP to create topology and coordinate files]]
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
* [[Preparing input files for a peptide using AMBER]] - detailed guide
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[Using Molfacture to edit molecules and add hydrogens]]
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide
* [[Symmetrising AMBER topology files]] - step by step guide for symmetrising a complex protein+ligand system
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb''
* [[Running GMIN with MD move steps AMBER]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Evaluating different components of AMBER energy function with SANDER]]
* [[Mutational BH steps]]
* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
* [[REMD with AMBER]]
* [[Performing a hydrogen-bond analysis]]
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Biomolecules in the energy landscape framework]]
* [[perm-prmtop.py]] - A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[Rotamer moves in AMBER]]
* [[Creating mismatched DNA duplex using NAB]]

=== [[aux2bib]] ===
To generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.
* [https://ctan.org/pkg/bibtools Get script here]

=== [[CamCasp]] ===
Cambridge package for Calculation of Anisotropic Site Properties
From Anthony Stone's website: 'CamCASP is a collection of scripts and programs written by Dr Alston Misquitta and myself for the calculation ab initio of distributed multipoles, polarizabilities, dispersion coefficients and repulsion parameters for individual molecules, and interaction energies between pairs of molecules using SAPT(DFT).'
* [http://www-stone.ch.cam.ac.uk/programs.html CamCASP home]
* [[CamCASP/Programming]]
* [[CamCASP/Programming/5/example1]]
* [[CamCASP/Notes]]
* [[CamCASP/Bugs]]
* [[CamCASP/ToDo/diskIO]]
* [[CamCASP/ToDo/Memory]]
* [[CamCASP/CodeExamples/DirectAccess]]

=== [[CPMD]] ===
Implementation of DFT for ''ab-initio'' molecular dynamics.
* [http://www.cpmd.org/ Home Page]
* [[CPMDInput]]

=== [[CHARMM]] ===
Molecular dynamics simulation program and associated force fields.
* [https://www.charmm.org/charmm/?CFID=65f7b3aa-8037-452a-bcd1-7583dd83a087&CFTOKEN=0 CHARMM]
* [[Generating pdb, crd and psf for a peptide sequence]]
* [[Converting between '.crd' and '.pdb']]
* [[Calculating energy of a conformation]]
* [[Calculating molecular properties]]
* [[Calculating order parameters]]
* [[CAMSHIFT]]
* [[Setting up (CHARMM)]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths (CHARMM)]]

=== [[disconnectionDPS]] ===
Produces disconnectivity graphs from min.data and ts.data files. This is included in the Wales group public tarball.
* [[Constructing Free Energy Disconnectivity Graphs]]

=== [[DMACRYS]] ===
Package which models crystals of rigid molecules.
* [http://www.chem.ucl.ac.uk/cposs/dmacrys/index.html Home Page]
* [[DMACRYS interface]]
* [[DMAGMIN setup]]
* [[PYGMIN & DMACRYS]]

=== [[GAMESS]] ===
General ''ab initio'' quantum chemistry package.
* [https://www.msg.chem.iastate.edu/gamess/ GAMESS]

=== [[Gaussian]] ===
General purpose package for computational chemistry calculations.
* [[Running an Gaussian03 interfaced OPTIM job]]

=== [[gnuplot]] ===
Open source graphing program.
* [http://www.gnuplot.info/ gnuplot]
* [[Plotting a quick histogram in gnuplot using the raw data]]
* [[Plotting data in real time]]
* [[Linear and non-linear regression in gnuplot]]

=== [[GROMACS]] ===
Molecular dynamics package.
* [[Installing GROMACS on Clust]]
* [http://www.mdtutorials.com/gmx/ External tutorials]
* [http://www.gromacs.org/Documentation/Tutorials More external tutorials]

=== [[HiRE-RNA]] ===
High-res course-grained energy model for RNA.
* [https://pubs.acs.org/doi/10.1021/jp102497y Explanatory Paper]

=== [[latex2html]] ===
Script which converts latex documents into HTML pages.
* [https://www.latex2html.org/ Get script here]

=== [[MMTSB-toolset]] ===
Group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD with CHARMM or AMBER.
* [http://feig.bch.msu.edu/mmtsb/Main_Page Documentation]
* [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html External tutorials]
* [[Installing and setting up the MMTSB toolset]]
* [[REX (Replica EXchange MD) with the MMTSB-toolset]]

=== [[Simulations using OPEP | OPEP]] ===
OPEP is a coarse-grained force field providing a potential for proteins and RNA.
* [http://opep.galaxy.ibpc.fr/ OPEP file generator here]
* [[Biomolecules in the energy landscape framework]]

=== [[pgprof]] ===
Profiler for portland-compiled codes
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

=== [[Pymol]] ===
Molecular visualisation program.
* [https://pymol.org/2/ PyMOL]
* [https://pymolwiki.org/index.php/Main_Page PyMOL Community Wiki]
* [[loading AMBER prmtop and inpcrd files into Pymol]]
* [[producing sexy ray-traced images]]
* [[advanced colouring]]
* [[Installing python modules]]
* [[PYGMIN & DMACRYS]]
* [[path2pdb.py]] - A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
=== [[VASP]] ===
OPTIM has an interface to VASP, which is installed on CSD3. In collaboration with Bora Karasulu the interface has been updated to use VASP format POSCAR input files for both single- and double-ended optimisations and path searches. The OPTIM odata file requires a line like

VASP 'mpirun -ppn 16 -np 16 /home/bk393/APPS/vasp.5.4.4/with-VTST/bin/vasp_std > vasp.out'

POSCAR files can be visualised using ase, the Atomic Simulation Environment, which can be accessed on volkhan via

module load anaconda/python3/5.3.0

pip install ase --user

ase-gui POSCAR1.vasp &

which assumes that ~/.input/bin is in your $PATH environment variable.

=== [[VMD]] ===
Molecular visualisation program.
* [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html Documentation]
* [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html External tutorials]
* [[using VMD to display and manipulate '.pdb' files]]
* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9
* [[visualising normal modes using VMD and OPTIM]]
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[Useful .vmdrc file]]
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
* [[VMD script to annotate each frame of a trajectory]]

=== [[xfig]] ===
Open source vector graphics editor
* [https://ctan.org/tex-archive/support/epstopdf/ Convert eps to pdf]

=== [[Xmakemol]] ===
Program for visualising atomic and molecular systems.
* [https://www.nongnu.org/xmakemol/ XMakemol]

=== [[xmgrace]] ===
2D plotting tool.
* [http://exciting-code.org/xmgrace-quickstart Xmgrace]

== Theoretical/Mathematical Notes ==

* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[Ellipsoid.model]]
* [[Ellipsoid.model.xyz]]
* [[Ellipsoid.xyz]]
* [[Gencoords]]
* [[GenCoords]]
* [[GenCoords Models]]
* [[Rotamer moves in AMBER]]
* [[Thomson problem in OPTIM]]

=== Angle-axis notes ===

* [[Angle-axis framework]]
* [[Computing normal modes in angle-axis]]

=== Rigid Bodies ===

* [[Automatic Rigid Body Grouping]]
* [[Rigid body input files for proteins using genrigid-input.py]]
* [[Local Rigid Body Framework]]
* [[Local rigid body in OPTIM]]

== Useful Scripts ==
* [[perm-prmtop.py]]: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[colourdiscon.py]]: A python program for sorting input for disconnectivity graphs
* [[pdb_to_movie.py]]: A python program to create an AMH movieseg file from a PDB file
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining
* [[recommended bash aliases]]
* [[David's .inputrc file]]
* [[Useful .vmdrc file]]
* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[GenCoords]]: A fortran program to generate coarse grain building blocks and initial coords using a set of geometric models.
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
See also the SCRIPTS/ directory in the SVN repository!
* [[Computing CHARMM FF energy using GMIN, MMTSB and CHARMM]] - Computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB options.
* [[Automatic Rigid Body Grouping]]
* [[ElaborateDiff]]
* [[Parameter-scanning script]]
* [[Pdb to movie.py]]
* [[VMD script to annotate each frame of a trajectory]]

== Useful links ==
* [http://www.ch.cam.ac.uk/computing/theory-compute-clusters The Theory Compute Clusters support page]. Contains useful cluster specific information, including example job submission scripts.

* A useful website which contains AMBER (GAFF) and OPLS parameters for small molecules. http://virtualchemistry.org/gmld.php . This could save us lot of time while trying to derive parameters on our own. If you are lucky, the molecule of your interest may already be there in the existing database. The topology files are in GROMACS format but possibly can be converted into AMBER parameter files. (script anyone ?)

* The moving-domain QM/MM method developed by Victor Batista's group http://gascon.chem.uconn.edu/software. This approach can be used in the derivation of charges for large proteins and nucleic acids, where a full-fledged ONIOM based calculation is comptutationally prohibitive. It has been applied to systems like the Gramicidin ion channel and Photosystem II.

== Miscellaneous ==
* [[Animated GIF on the group website]]
* [[Backup strategy]]
* [[Chain crossing]]
* [[Computer Office services]]
* [[Computing values only once]]
* [[Decoding heat capacity curves]]
* [[Differences from Clust]]
* [[Fixing thunderbird links]]
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Intel Trace Analyzer and Collector]]
* [[LDAP plans]]
* [[Lapack compilation]]
* [[Mek-quake Queueing system]]
* [[Mek-quake initial setup notes]]
* [[New mek-quake]]
* [[Maui compilation]]
* [[Torque and Maui]]
* [[Mercurial]]
* [[Migrating to the new SVN server]]
* [[NECI Parallelization]]
* [[Optimization tricks]]
* [[Other IT stuff]]
* [[Porfuncs Documentation]]
* [[Progress]]
* [[Proposed changes to backup and archiving]]
* [[Rama upgrade]]
* [[Remastering Knoppix]]
* [[See unpacked nodes]]
* [[Tardis scheduling policy]]
* [[Zippo Sicortex machine]]
* [[Beginner's guide to working in Wales group]]

== Useful linux stuff ==

===Basics===
* [[basic linux commands everyone should know!]]
* [[piping and redirecting output from one command or file to another]] - how to save yourself hours!
* [[bash loop tricks]]
* [[bash history searching]]

===Remote access===
* [[setting up aliases to quickly log you in to a different machine]]
* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''
* [[using 'ssh-keygen' to automatically log you into clusters from your workstation]] (no more typing in your password!)
* [[mounting sharedscratch locally]]

===Find and replace===
* [[short 'sed' examples]]
* [[quick guide to awk]]
* [[short 'awk' examples]]

===File manipulation===
* [[sorting a file by multiple columns]]
* [[using tar and gzip to compress/uncompress files | using tar and bzip2 to compress/uncompress files]]
* [[conversion between different data file formats]] -'almost one-line' scripts
* [[conversion between different image file formats]] - the ''convert'' command
* [[removing an excessive number of files from a directory - when 'rm' just isn't enough]]

===Cluster queues===
* [[submitting jobs, interactively or to a cluster queue system]]
* [[identifying job on a node]] - if you need to kill only one of few running jobs
* [[getting started with SLURM]]
* [[a guide to using SLURM to run PATHSAMPLE]]
* [[a guide to using SLURM to run GPU jobs on pat]]
* [[managing interactive jobs on cluster]]

===Miscellaneous/uncategorised===
* [[installing packages on your managed CUC3 workstation]]
* [[running programs in the background]] - so you can use your shell for other things at the same time
* [[finding bugs in latex documents that will not compile]]
* [[printing files from the command line using 'lpr']]
* [[uploading non image files to the wiki]]

== Compiler Flags ==

* [[Compiler Flags]]
* [[Blacklisting Compilers]]
* [[Lapack compilation]]
* [[Pdb to movie.py]]
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

== SuSE ==

* [[Upgrading destiny]]
* [[Upgrading sword]]
* [[SuSE 10.1 workstation image]]
* [[SuSE 10.2 workstation image]]
* [[SuSE 10.3 workstation image]]
* [[SuSE 11.1]]

--[[User:adk44|adk44]] 17.00, 9 May 2019 (BST)

Preparing input files for a peptide using AMBER

2021-10-12T09:11:07Z

Nn320: /* Step 3: Minimising the structure using sander */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/nn320/amber14/lib
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that for running sander you need to ensure you have the appropriate library files in your $LD_LIBRARY_PATH. You should already have sander working if you followed Step 0. In case, sander does not run automatically, alternatively, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-12T09:08:24Z

Nn320: /* Step 0: Have amber on your system */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/nn320/amber14/lib
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation. In case, sander does not run automatically, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T14:42:30Z

Nn320: /* Step 3: Minimising the structure using sander */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation. In case, sander does not run automatically, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T14:39:08Z

Nn320: /* Step 3: Minimising the structure using sander */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation. In case, sander does not run automatically, you need to first build amber.
First update your $LD_LIBRARY_PATH to include $AMBERHOME/lib by including the following in ~/.bashrc
<pre>export LD_LIBRARY_PATH="${AMBERHOME}/lib:${LD_LIBRARY_PATH}"
export PYTHONPATH="${AMBERHOME}/lib/python2.7/site-packages:${PYTHONPATH}"</pre>

Then on the command line run
<pre>source ~/.bashrc</pre>
Then run the configure script with GNU as the compiler:
<pre>./configure gnu</pre>

After configuring, run
<pre>make install</pre>
to finish building amber.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T14:17:18Z

Nn320: /* Step 8: Creating atomgroups file */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===
The atomgroups file is required when the GROUPROTATION keyword is included in the data file.
To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself. The hint is that for an amino acid residue NH2-CH-(CH2-R)-CO- the rotation axis is defined using the central C (C alpha) and the C of side chain, the group is defined using the atoms H2 and R in the group CH2-R.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T14:13:23Z

Nn320: /* Step 7: Creating topology file for modified force field ff99IDPs */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (old_symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T10:46:35Z

Nn320: /* Step 4: Symmetrise the topology file so obtained */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/. Please note that, you should have a look at https://wikis.ch.cam.ac.uk/ro-walesdocs/wiki/index.php/Setting_up if you do not have your peptide capped with ACE and NME groups. For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T10:16:02Z

Nn320: /* Step 8: Creating atomgroups file */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself.
You may want to visualise the molecule in pymol with atom numbers to write the atomgroups file. A pymol script label_atom_numbers.pml could have
<pre>
load minncrst.pdb, mol
show sticks
show sphere
set sphere_scale, 0.3
set label_size, 10
set label_font_id, 9
set ray_trace_fog, 0
set ray_shadows, 0
unset depth_cue
bg_color white
set antialias, 2
set hash_max, 300
set ray_trace_mode, 3
set ray_trace_color, black
set ray_opaque_background, off
</pre>
When you run the following from command line on your local workstation,
<pre>pymol label_atom_numbers.pml</pre>
A pymol window appears with the molecule loaded in. On the rightmost there is object control panel with several buttons A,S,H,L,C. From the L (label button) select atom identifiers and then select ID. If you want to save the molecule as png, on the pymol command line run,
<pre>ray 2000, 1500
png raytraced_minncrst.png, dpi=300</pre>

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can have
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T09:30:15Z

Nn320: /* Step 6: Check symmetrisation */

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

Step 6a: Creation of several coords.inpcrd files with permuted atoms

Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-11T09:27:28Z

Nn320:

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

===Step 0: Have amber on your system===

You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc on nest.ch.private.cam.ac.uk.
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

===Step 1: Make topology and coordinates file using tleap in AMBER===

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

===Step 2: Check the amber library files===

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

===Step 3: Minimising the structure using sander===
Please note that sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation.

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

===Step 4: Symmetrise the topology file so obtained===

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

===Step 5: Creating a perm.allow file===
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

===Step 6: Check symmetrisation===

=====Step 6a:=====
Creation of several coords.inpcrd files with permuted atoms
=====Step 6b:=====
Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
RADIUS 1000.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

===Step 7: Creating topology file for modified force field ff99IDPs===

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

===Step 8: Creating atomgroups file===

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

===Miscellaneous===

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-09T15:15:54Z

Nn320:

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

Step 0: Have amber on your system (nest.ch.private.cam.ac.uk)
You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

Step 3: Minimising the structure using sander (sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation)

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

Step 5: Creating a perm.allow file
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, sbatch_GMIN_serial_nest for it. You will need to copy all these files to the group directories created when you ran symm_check.sh script. To automate this copying, you can create a directory gmin_input_files and put coords.prmtop, min.in, data, sbatch_GMIN_serial_nest files in it and create a bash script copy_gmin_input_files.sh that has
<pre>
#!/bin/bash
total_groups=`head -n 1 perm.allow`
cp gmin_input_files/* all_group_one_pair/
cd all_group_one_pair
sbatch sbatch_GMIN_serial_nest
cd ../
for ((i=1;i<=$total_groups;i++));
do
cp gmin_input_files/* group$i/
cd group$i
sbatch sbatch_GMIN_serial_nest
cd ../
done
</pre>
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
MAXIT 1 1
MAXBFGS 0.0D0
STEP 0.0 0.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general sbatch_GMIN_serial_nest can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-09T14:59:54Z

Nn320:

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

Step 0: Have amber on your system (nest.ch.private.cam.ac.uk)
You can obtain amber14 directory from someone's home directory on sinister or from /home/nn320/amber14 on nest.
You can have AMBER in your path by having something similar to this in ~/.bashrc
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

Step 3: Minimising the structure using sander (sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation)

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

Step 5: Creating a perm.allow file
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, submission_script for it. You will need to copy all these files to the group directories created by when you ran symm_check.sh script.
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
STEP 0.0 0.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general submission_script can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-09T14:57:46Z

Nn320:

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

Step 0: Have amber on your system (nest.ch.private.cam.ac.uk)

Assuming you have AMBER in your path by having something similar to this in ~/.bashrc
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

Step 3: Minimising the structure using sander (sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation)

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

Step 5: Creating a perm.allow file
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, submission_script for it. You will need to copy all these files to the group directories created by when you ran symm_check.sh script.
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
STEP 0.0 0.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general submission_script can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-09T14:57:18Z

Nn320:

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

Step 0: Having amber on your system (nest.ch.private.cam.ac.uk)

Assuming you have AMBER in your path by having something similar to this in ~/.bashrc
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol old_mol.pdb
quit
</pre>
Run, <pre>tleap -f leap.in</pre>
This gives pdb, prmtop and incprd files as output.
Note that the pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

Step 3: Minimising the structure using sander (sander does not work on nest, it will probably work on your local workstation, you need to repeat Step 0 on your local workstation)

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p old_coords.prmtop -c old_coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise old_coords.inpcrd, just look at old_mol.pdb or use
<pre>$AMBERHOME/bin/ambpdb -p old_coords.prmtop -c old_coords.inpcrd > old_coords_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your coords.inpcrd file.
So, now you have obtained your old_coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.ff03.py script. It is written in python2, so first run.
<pre>module load anaconda/python2/5.3.0</pre>
Its usage is
<pre>perm-prmtop.ff03.py old_coords.prmtop old_symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check for correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

Step 5: Creating a perm.allow file
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/
Run
<pre>perm-pdb.py old_mol.pdb AMBER</pre>

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh. If you have python2 module loaded already, you will have to remove it and load python3 before running symm_check.sh since it is a hybrid bash and python script.
You would need A12GMIN executable, min.in, data, old_symmetrised_coords.prmtop (rename it as coords.prmtop for use with A12GMIN), perm.allow, submission_script for it. You will need to copy all these files to the group directories created by when you ran symm_check.sh script.
The min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Data file can have
<pre>
STEPS 1 1.0
DEBUG
STEP 0.0 0.0
SLOPPYCONV 1.0D-6
TIGHTCONV 1.0D-6
TEMPERATURE 0.5962
AMBER12
</pre>
A general submission_script can look like,
<pre>
#!/bin/bash

#SBATCH --job-name=symm_check
#SBATCH --ntasks=1 # Specify the number of nodes you want to run on
##SBATCH --requeue # Requeue job in the case of node failure
#SBATCH --mail-type=FAIL # Receive an email if your job fails
#SBATCH --time=5-00:00:00

echo "Time: `date`" > jobnumber

echo $SLURM_NTASKS > nodes.info
srun hostname >> nodes.info
echo $USER >> nodes.info
pwd >> nodes.info

/sharedscratch/crsid/softwarewales/GMIN/builds/gfortran_serial_nest/A12GMIN >> output

echo Finished at `date` >> jobnumber
</pre>
You can then use
<pre>grep -i "Lowest minimum" group*/output</pre>
If all the energies are same, you can stop here, you have successfully created coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-08T08:17:47Z

Nn320:

The steps given below are when you are trying to use one of the AMBER force fields to create topology file (coords.prmtop) and coordinates file (coords.inpcrd) for use with GMIN, OPTIM and PATHSAMPLE.

Step 0: Having amber on your system

Assuming you have AMBER in your path by having something similar to this in ~/.bashrc
<pre>
export AMBERHOME=/home/crsid/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

Run, <pre>tleap -f leap.in</pre>
leap.in file specifies force field, sequence and solvent model.
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop old_coords.inpcrd
savepdb mol mol.pdb
quit
</pre>
This gives a pdb, prmtop and incprd files as output
Note that pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94.lib, all_amino94ildn.lib, all_aminoct94ildn.lib, all_aminont94ildn.lib, ions94.lib and solvents.lib get loaded.
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are probably correct.
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
amber14/dat/leap/lib> 1 0 0 0 0 0
softwarewales/AMBERTOOLS/dat/leap/lib/all_aminoct94.lib> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of lib files in amber14/dat/leap/lib/ somewhere and replace the lib files in the original directory with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new old_coords.prmtop and old_coords.inpcrd file before proceeding to Step 3.

Step 3: Minimising the structure using sander

This is to ensure that coordinates file has a physical structure without atom overlaps.
For running sander, you just require, old_coords.prmtop, old_coords.inpcrd and min.in file. Note that you will have to run this in a separate directory with old_coords.prmtop and old_coords.inpcrd files renamed as coords.prmtop and coords.inpcrd respectively. Softwares like AMBER and GMIN are very particular about file names and they accept coords.prmtop and coords.inpcrd as input files.
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p coords.prmtop -c coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise min.ncrst and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise older coords.inpcrd, just use the above command replacing coordinate file and the output file, i.e.
<pre>$AMBERHOME/bin/ambpdb -p coords.prmtop -c coords.inpcrd > old_inpcrd.pdb </pre>
Use the min.ncrst so obtained as your new coords.inpcrd file.
So, now you have obtained your coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the ff99SBildn force field use perm-prmtop.py script. It is written in python2.
Its usage is
<pre>perm-prmtop.py old_coords.prmtop symmetrised_coords.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy of the molecule does not change.
The best way to check correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy for each of them to get the same energy.

Step 5: Creating a perm.allow file

Run
<pre>perm-pdb.py mol.pdb AMBER</pre>
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/

To check the perm.allow file simply read the documentation of PERMDIST in GMIN
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh

You can probably stop here, you have coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to change the permission of the python file before running them using
``chmod 755 ADD_CMAP.py``
Obtain another prmtop file which should already be symmetrised by following these steps.
You will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop (symmetrised_coords.prmtop) and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files or on the github wesbite for ff99IDPs.
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and AMBER energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions under SCEE and SCNB flags. The A12GMIN program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-08T07:53:30Z

Nn320:

How to create input files for a peptide for use with GMIN?

The steps given below are when you are trying to use one of the AMBER force fields.

Step 0: Having amber on your system

Assuming you have AMBER in your path by having something similar to this in ~/.bashrc
<pre>
export AMBERHOME=/home/nn320/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

Run, <pre>tleap -f leap.in</pre>
leap.in file specifies force field, sequence, solvent model
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop coords.inpcrd
savepdb mol mol.pdb
quit
</pre>
This gives a pdb, prmtop and incprd files as output
Note that pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94, all_amino94ildn, all_aminoct94ildn, all_aminont94ildn, ions94, solvents.lib
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are correct
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 0 0 0 0 0
softwareWales ambertools> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 0 0 0 0 0
softwareWales ambertools> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of amber lib files somewhere and replace them with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new coords.prmtop and coords.inpcrd file.

Step 3: Minimising the structure using sander

This is to ensure that coordinate file has a physical structure without atom overlaps.
For running sander, you just require, coords.prmtop, coords.inpcrd, min.in file
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p coords.prmtop -c coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise it and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise older coords.inpcrd, just use the above command replacing coordinate file and the output file.

Use the min.ncrst so obtained as your new coords.inpcrd file.
So, now you have obtained your coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the above force field use perm-prmtop.py script. It is written in python2.
Its usage is
<pre>perm-prmtop.py old.prmtop symmetrised.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy should not change
The best way to check correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy of each of them to get the same energy.

Step 5: Creating a perm.allow file

Run
<pre>perm-pdb.py name.pdb AMBER</pre>
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/

To check the perm.allow file simply read the documentation of PERMDIST
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh

You can probably stop here, you have coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to make the python files executable
chmod 755 ADD_CMAP.py
Obtain another prmtop file
This should already be symmetrised
The command to use is, you will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and GMIN energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions. The program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Preparing input files for a peptide using AMBER

2021-10-07T16:05:59Z

Nn320:

How to create input files for a peptide for use with GMIN?

The steps given below are when you are trying to use one of the AMBER force fields.

Step 0: Having amber on your system

Assuming you have AMBER in your path by having something similar to this in ~/.bashrc
<pre>
export AMBERHOME=/home/nn320/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH
</pre><pre>
Then run, <pre>source ~/.bashrc</pre> in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

Run, <pre>tleap -f leap.in</pre>
leap.in file specifies force field, sequence, solvent model
My leap.in file has the following lines.
<pre>
source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop coords.inpcrd
savepdb mol mol.pdb
quit
</pre>
This gives a pdb, prmtop and incprd files as output
Note that pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94, all_amino94ildn, all_aminoct94ildn, all_aminont94ildn, ions94, solvents.lib
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are correct
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 0 0 0 0 0
softwareWales ambertools> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 0 0 0 0 0
softwareWales ambertools> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of amber lib files somewhere and replace them with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new coords.prmtop and coords.inpcrd file.

Step 3: Minimising the structure using sander

This is to ensure that coordinate file has a physical structure without atom overlaps.
For running sander, you just require, coords.prmtop, coords.inpcrd, min.in file
min.in file can have something like,
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Then on the command line run,
<pre>
$AMBERHOME/bin/sander -O -i min.in -o min.out -p coords.prmtop -c coords.inpcrd -r min.ncrst</pre>
The min.ncrst has minimised geometry.
To visualise it and compare it with initial geometry run the following,
<pre>$AMBERHOME/bin/ambpdb -p coords.prmtop -c min.ncrst > minncrst.pdb </pre>
To visualise older coords.inpcrd, just use the above command replacing coordinate file and the output file.

Use the min.ncrst so obtained as your new coords.inpcrd file.
So, now you have obtained your coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the above force field use perm-prmtop.py script. It is written in python2.
Its usage is
<pre>perm-prmtop.py old.prmtop symmetrised.prmtop</pre>

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy should not change
The best way to check correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy of each of them to get the same energy.

Step 5: Creating a perm.allow file

Run
<pre>perm-pdb.py name.pdb AMBER</pre>
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/

To check the perm.allow file simply read the documentation of PERMDIST
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh

You can probably stop here, you have coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to make the python files executable
chmod 755 ADD_CMAP.py
Obtain another prmtop file
This should already be symmetrised
The command to use is, you will have to unload python2 and load python3 module.
<pre>python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
or
<pre>python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s</pre>
Here, amber.prmtop represents the symmetrised prmtop and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and GMIN energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
<pre>
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/
</pre>
Example data file can be
<pre>
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12
</pre>

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions. The program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

Comprehensive Contents Page

2021-10-07T16:01:36Z

Nn320: /* AMBER */

This page is designed to organise all of the pages on this wiki, as well as provide other useful links. Note that some pages may appear under more than one heading.

== Getting Started ==
[[Wales Group]] provides good step-by-step instructions. Relevant pages are:

=== Acquiring and compiling the group software ===
* [[SVN setup]]
* [[Git Workflow]]
* [[Wales Group Version control]] - to keep the code standardised.
* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.
* [[Compiling Wales Group codes using cmake]] - CMake (Cross-platform Make) allows us to compile and test the group codebase regardless of platform. This page provides crucial information how to compile using cmake.
* [[ElaborateDiff]]

=== Maintaining code health ===
* [[Jenkins CI]] - explains Jenkins, which we use to download our code and compile each of our targets with each of the compilers every night.
* https://wales-jenkins.ch.cam.ac.uk/ - log for our Jenkins tests.
* [[Branching and Merging]]
* [[Cmake interface building]]
* [[Installing python modules]]
* [[Revamping the modules system]]

=== Collaborators without access to the SVN repository ===
For licensing reasons, some code cannot be included in the Wales Group public tarball.
* http://www-wales.ch.cam.ac.uk/svn.tar.bz2 - Wales group public tarball. Includes [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]].
If a collaborator has a [[CHARMM]] or [[AMBER]] licence, we do maintain separate tarballs which include the [[CHARMM]], [[AMBER]] and [[CHARMM]]+[[AMBER]] source and interfaces. These are not linked anywhere on the website and require a username ('''wales''') and password ('''group''') to download:

* [http://www-wales.ch.cam.ac.uk/CHARMM/svn.CHARMM.tar.bz2 CHARMM]
* [http://www-wales.ch.cam.ac.uk/AMBER/svn.AMBER.tar.bz2 AMBER]
* [http://www-wales.ch.cam.ac.uk/both/svn.both.tar.bz2 AMBER+CHARMM]

=== Running on Windows ===
Not particularly recommended.
* [[Running Wales Group software on Windows 7]]

== Wales Group Programs ==

=== Programs ===
* [[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
* [[OPTIM]]: A program for optimizing geometries and calculating reaction pathways.
* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.
* [[DISCOTRESS]]: A program to perform detailed quantitative analysis of a kinetic network (stationary point database)

=== Curated Examples ===
* https://github.com/wales-group/examples - set of tutorials detailing how to use GMIN, OPTIM and PATHSAMPLE. Essential for beginners.
* http://www-wales.ch.cam.ac.uk/VM/Wales_Group_VM.ova - Pre-prepared teaching virtual machine. This contains the code and examples.
* https://www.virtualbox.org/wiki/Downloads - This is required if using the VM above.
* https://github.com/wales-group/examples.git - Alternatively, you can run the examples on your own machine. To get hold of the relevant files:
<pre>
git clone https://github.com/wales-group/examples.git
</pre>

== Useful Notes on Wales Group Programs and Subroutines ==
=== [[GMIN]] ===
* [[Adding a model to GMIN]] - rough outline of the subroutines that need to be changed to add a new model to GMIN
* [[Compiling Wales Group codes using cmake | Compiling GMIN using cmake ]]
* [[Selecting search parameters for GMIN]]
* [[Global optimization of biomolecules using CHARMM]]
* [[Global optimization of biomolecules using AMBER9]]
* [[Global optimization of biomolecules using AMBER9 with Structural Restraints]]
* [[Calculating binding free energy using the FSA method]]
* [[Restarting a GMIN run from a dump file]]
* [[Using the implicit membrane model IMM1]]
* [[Running a Go model with the AMHGMIN]]
* [[Running a G\=o model with the AMHGMIN]]
* [[Ligand binding-mode searches with HBONDMATRIX]]
* [[Compiling and using GMIN with QUIP]]
* [[Using GMIN and OPTIM with GPUs]]
* [[Using GMIN to generate endpoints]]
* [[Using GMIN to generate endpoints (CHARMM)]]
* [[Generating a GMIN Eclipse project]]
* [[Mutational BH steps]]
* [[Biomolecules in the energy landscape framework]]
* [[DMAGMIN setup]]
* [[Keywords]]
* [[PYGMIN & DMACRYS]]
* [[Rotamer moves in AMBER]]
* [[Python interface for GMIN/OPTIM]]

==== Scripts ====
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining

==== Useful info for coding GMIN ====
* [[Program flow]] - contains information about what the various files in GMIN do and what order they're called.
* [[amberinterface]]

==== Projects ====
* [[GMIN MOVES module]]
* [[GMIN SANITY module]]
* [[GMIN TESTS module]]
* [[CAMSHIFT]]

=== [[OPTIM]] ===
* [[Adding a model to OPTIM]] - rough outline of the subrounties that need to be changed to add a new model to OPTIM
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[visualising normal modes using VMD and OPTIM]]
* [[Compiling Wales Group codes using cmake | Compiling OPTIM using cmake ]]
* [[OPTIM/Q-Chem Tutorial]]
* [[OPTIM and PY ellipsoids tutorial]]
* [[OPTIM output files]]
* [[Minimizing a structure using OPTIM and AMBER9]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Creating movies (.mpg) of paths using OPTIM]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Debugging odd transition states in OPTIM]]
* [[Connecting two minima with a pathway]] - step by step
* [[Compiling and using OPTIM with QUIP]]
* [[Running an Gaussian03 interfaced OPTIM job]]
* [[The effect of calculating less than the maximum number of eigenvalues using ENDHESS n]]
* [[Biomolecules in the energy landscape framework]]
* [[BLJ60 example setup]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Python interface for GMIN/OPTIM]]
* [[Thomson problem in OPTIM]]
* [[Instanton tunneling and classical rate calculations with OPTIM]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[common setup problem : No Frequency Warning]]

=== [[PATHSAMPLE]] ===
* [[Adding a model to PATHSAMPLE]] - rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[Compiling Wales Group codes using cmake | Compiling PATHSAMPLE using cmake ]]
* [[IMPORTANT: Using PATHSAMPLE safely on sinister]]
* [[Adding a model for PATHSAMPLE]]
* [[List of output files for PATHSAMPLE]]
* [[Using BHINTERP to find minima between two end points]]
* [[Finding an initial path between two end points (minima)]]
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[Optimising a path]]
* [[Fine tuning UNTRAP]] - ensuring that it picks sensible minima
* [[Calculating rate constants (GT and fastest path)]]
* [[Calculating rate constants (SGT, DGT, and SDGT)]]
* [[Identifying the k fastest paths between endpoints using KSHORTESTPATHS]]
* [[Removing minima and transition states from the database]]
* [[Relaxing existing minima with new potential and creating new database]]
* [[Relaxing existing transition states with new potential and creating new database]]
* [[If things go wrong...]]
* [[If you lost file min.data, but still you have points.min]]
* [[path.info file is not read, causes PATHSAMPLE to die]]
* [[BLJ60 example setup]]
* [[When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path]]
* [[Biomolecules in PATHSAMPLE]]
* [[Biomolecules in the energy landscape framework]]
* [[Expanding the kinetic transition network with PATHSAMPLE]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths]]
* [[Pathsampling short paths (CHARMM)]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[Connecting Sub-databases]]
* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
* [[STARTING INITIAL PATH JOBS WITH PATHSAMPLE]]: How to start initial path jobs with PATHSAMPLE if no min.data or path.info files are present.

=== [[Notes on MINPERMDIST | MINPERMDIST]] ===

=== [[Quasi-continuous interpolation for biomolecules | QCI]] ===

=== [[DISCOTRESS | Detailed kinetic network analysis with DISCOTRESS]] ===

== Non-Group Software ==

=== [[AMBER]] ===
Molecular dynamics simulation program and associated force fields.
* [http://ambermd.org/ AMBER]
* [http://ambermd.org/tutorials/ AMBER tutorials] - recommended reading for '''ANYONE''' using AMBER!
* [[Notes on AMBER 12 interface]]
* [[Using AMBER 14 on the GPU and compute clusters]]
* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
* [[Generating parameters using RESP charges from GAMESS-US]]
* [[Simple scripts for LEaP to create topology and coordinate files]]
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
* [[Preparing input files for a peptide using AMBER]] - detailed guide
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[Using Molfacture to edit molecules and add hydrogens]]
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide
* [[Symmetrising AMBER topology files]] - step by step guide for symmetrising a complex protein+ligand system
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb''
* [[Running GMIN with MD move steps AMBER]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Evaluating different components of AMBER energy function with SANDER]]
* [[Mutational BH steps]]
* [[CHECKSPMUTATE]]: An extension of CHECKSPODATA which allows for a protein to be mutated or transformed into a homologue.
* [[Pathway Gap Filling Post-CHECKSPMUTATE]]: Post-processing following CHECKSPMUTATE
* [[REMD with AMBER]]
* [[Performing a hydrogen-bond analysis]]
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Biomolecules in the energy landscape framework]]
* [[perm-prmtop.py]] - A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[Rotamer moves in AMBER]]
* [[Creating mismatched DNA duplex using NAB]]

=== [[aux2bib]] ===
To generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.
* [https://ctan.org/pkg/bibtools Get script here]

=== [[CamCasp]] ===
Cambridge package for Calculation of Anisotropic Site Properties
From Anthony Stone's website: 'CamCASP is a collection of scripts and programs written by Dr Alston Misquitta and myself for the calculation ab initio of distributed multipoles, polarizabilities, dispersion coefficients and repulsion parameters for individual molecules, and interaction energies between pairs of molecules using SAPT(DFT).'
* [http://www-stone.ch.cam.ac.uk/programs.html CamCASP home]
* [[CamCASP/Programming]]
* [[CamCASP/Programming/5/example1]]
* [[CamCASP/Notes]]
* [[CamCASP/Bugs]]
* [[CamCASP/ToDo/diskIO]]
* [[CamCASP/ToDo/Memory]]
* [[CamCASP/CodeExamples/DirectAccess]]

=== [[CPMD]] ===
Implementation of DFT for ''ab-initio'' molecular dynamics.
* [http://www.cpmd.org/ Home Page]
* [[CPMDInput]]

=== [[CHARMM]] ===
Molecular dynamics simulation program and associated force fields.
* [https://www.charmm.org/charmm/?CFID=65f7b3aa-8037-452a-bcd1-7583dd83a087&CFTOKEN=0 CHARMM]
* [[Generating pdb, crd and psf for a peptide sequence]]
* [[Converting between '.crd' and '.pdb']]
* [[Calculating energy of a conformation]]
* [[Calculating molecular properties]]
* [[Calculating order parameters]]
* [[CAMSHIFT]]
* [[Setting up (CHARMM)]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths (CHARMM)]]

=== [[disconnectionDPS]] ===
Produces disconnectivity graphs from min.data and ts.data files. This is included in the Wales group public tarball.
* [[Constructing Free Energy Disconnectivity Graphs]]

=== [[DMACRYS]] ===
Package which models crystals of rigid molecules.
* [http://www.chem.ucl.ac.uk/cposs/dmacrys/index.html Home Page]
* [[DMACRYS interface]]
* [[DMAGMIN setup]]
* [[PYGMIN & DMACRYS]]

=== [[GAMESS]] ===
General ''ab initio'' quantum chemistry package.
* [https://www.msg.chem.iastate.edu/gamess/ GAMESS]

=== [[Gaussian]] ===
General purpose package for computational chemistry calculations.
* [[Running an Gaussian03 interfaced OPTIM job]]

=== [[gnuplot]] ===
Open source graphing program.
* [http://www.gnuplot.info/ gnuplot]
* [[Plotting a quick histogram in gnuplot using the raw data]]
* [[Plotting data in real time]]
* [[Linear and non-linear regression in gnuplot]]

=== [[GROMACS]] ===
Molecular dynamics package.
* [[Installing GROMACS on Clust]]
* [http://www.mdtutorials.com/gmx/ External tutorials]
* [http://www.gromacs.org/Documentation/Tutorials More external tutorials]

=== [[HiRE-RNA]] ===
High-res course-grained energy model for RNA.
* [https://pubs.acs.org/doi/10.1021/jp102497y Explanatory Paper]

=== [[latex2html]] ===
Script which converts latex documents into HTML pages.
* [https://www.latex2html.org/ Get script here]

=== [[MMTSB-toolset]] ===
Group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD with CHARMM or AMBER.
* [http://feig.bch.msu.edu/mmtsb/Main_Page Documentation]
* [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html External tutorials]
* [[Installing and setting up the MMTSB toolset]]
* [[REX (Replica EXchange MD) with the MMTSB-toolset]]

=== [[Simulations using OPEP | OPEP]] ===
OPEP is a coarse-grained force field providing a potential for proteins and RNA.
* [http://opep.galaxy.ibpc.fr/ OPEP file generator here]
* [[Biomolecules in the energy landscape framework]]

=== [[pgprof]] ===
Profiler for portland-compiled codes
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

=== [[Pymol]] ===
Molecular visualisation program.
* [https://pymol.org/2/ PyMOL]
* [https://pymolwiki.org/index.php/Main_Page PyMOL Community Wiki]
* [[loading AMBER prmtop and inpcrd files into Pymol]]
* [[producing sexy ray-traced images]]
* [[advanced colouring]]
* [[Installing python modules]]
* [[PYGMIN & DMACRYS]]
* [[path2pdb.py]] - A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
=== [[VASP]] ===
OPTIM has an interface to VASP, which is installed on CSD3. In collaboration with Bora Karasulu the interface has been updated to use VASP format POSCAR input files for both single- and double-ended optimisations and path searches. The OPTIM odata file requires a line like

VASP 'mpirun -ppn 16 -np 16 /home/bk393/APPS/vasp.5.4.4/with-VTST/bin/vasp_std > vasp.out'

POSCAR files can be visualised using ase, the Atomic Simulation Environment, which can be accessed on volkhan via

module load anaconda/python3/5.3.0

pip install ase --user

ase-gui POSCAR1.vasp &

which assumes that ~/.input/bin is in your $PATH environment variable.

=== [[VMD]] ===
Molecular visualisation program.
* [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html Documentation]
* [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html External tutorials]
* [[using VMD to display and manipulate '.pdb' files]]
* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9
* [[visualising normal modes using VMD and OPTIM]]
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[Useful .vmdrc file]]
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
* [[VMD script to annotate each frame of a trajectory]]

=== [[xfig]] ===
Open source vector graphics editor
* [https://ctan.org/tex-archive/support/epstopdf/ Convert eps to pdf]

=== [[Xmakemol]] ===
Program for visualising atomic and molecular systems.
* [https://www.nongnu.org/xmakemol/ XMakemol]

=== [[xmgrace]] ===
2D plotting tool.
* [http://exciting-code.org/xmgrace-quickstart Xmgrace]

== Theoretical/Mathematical Notes ==

* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[Ellipsoid.model]]
* [[Ellipsoid.model.xyz]]
* [[Ellipsoid.xyz]]
* [[Gencoords]]
* [[GenCoords]]
* [[GenCoords Models]]
* [[Rotamer moves in AMBER]]
* [[Thomson problem in OPTIM]]

=== Angle-axis notes ===

* [[Angle-axis framework]]
* [[Computing normal modes in angle-axis]]

=== Rigid Bodies ===

* [[Automatic Rigid Body Grouping]]
* [[Rigid body input files for proteins using genrigid-input.py]]
* [[Local Rigid Body Framework]]
* [[Local rigid body in OPTIM]]

== Useful Scripts ==
* [[perm-prmtop.py]]: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[colourdiscon.py]]: A python program for sorting input for disconnectivity graphs
* [[pdb_to_movie.py]]: A python program to create an AMH movieseg file from a PDB file
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining
* [[recommended bash aliases]]
* [[David's .inputrc file]]
* [[Useful .vmdrc file]]
* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[GenCoords]]: A fortran program to generate coarse grain building blocks and initial coords using a set of geometric models.
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
See also the SCRIPTS/ directory in the SVN repository!
* [[Computing CHARMM FF energy using GMIN, MMTSB and CHARMM]] - Computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB options.
* [[Automatic Rigid Body Grouping]]
* [[ElaborateDiff]]
* [[Parameter-scanning script]]
* [[Pdb to movie.py]]
* [[VMD script to annotate each frame of a trajectory]]

== Useful links ==
* [http://www.ch.cam.ac.uk/computing/theory-compute-clusters The Theory Compute Clusters support page]. Contains useful cluster specific information, including example job submission scripts.

* A useful website which contains AMBER (GAFF) and OPLS parameters for small molecules. http://virtualchemistry.org/gmld.php . This could save us lot of time while trying to derive parameters on our own. If you are lucky, the molecule of your interest may already be there in the existing database. The topology files are in GROMACS format but possibly can be converted into AMBER parameter files. (script anyone ?)

* The moving-domain QM/MM method developed by Victor Batista's group http://gascon.chem.uconn.edu/software. This approach can be used in the derivation of charges for large proteins and nucleic acids, where a full-fledged ONIOM based calculation is comptutationally prohibitive. It has been applied to systems like the Gramicidin ion channel and Photosystem II.

== Miscellaneous ==
* [[Animated GIF on the group website]]
* [[Backup strategy]]
* [[Chain crossing]]
* [[Computer Office services]]
* [[Computing values only once]]
* [[Decoding heat capacity curves]]
* [[Differences from Clust]]
* [[Fixing thunderbird links]]
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Intel Trace Analyzer and Collector]]
* [[LDAP plans]]
* [[Lapack compilation]]
* [[Mek-quake Queueing system]]
* [[Mek-quake initial setup notes]]
* [[New mek-quake]]
* [[Maui compilation]]
* [[Torque and Maui]]
* [[Mercurial]]
* [[Migrating to the new SVN server]]
* [[NECI Parallelization]]
* [[Optimization tricks]]
* [[Other IT stuff]]
* [[Porfuncs Documentation]]
* [[Progress]]
* [[Proposed changes to backup and archiving]]
* [[Rama upgrade]]
* [[Remastering Knoppix]]
* [[See unpacked nodes]]
* [[Tardis scheduling policy]]
* [[Zippo Sicortex machine]]
* [[Beginner's guide to working in Wales group]]

== Useful linux stuff ==

===Basics===
* [[basic linux commands everyone should know!]]
* [[piping and redirecting output from one command or file to another]] - how to save yourself hours!
* [[bash loop tricks]]
* [[bash history searching]]

===Remote access===
* [[setting up aliases to quickly log you in to a different machine]]
* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''
* [[using 'ssh-keygen' to automatically log you into clusters from your workstation]] (no more typing in your password!)
* [[mounting sharedscratch locally]]

===Find and replace===
* [[short 'sed' examples]]
* [[quick guide to awk]]
* [[short 'awk' examples]]

===File manipulation===
* [[sorting a file by multiple columns]]
* [[using tar and gzip to compress/uncompress files | using tar and bzip2 to compress/uncompress files]]
* [[conversion between different data file formats]] -'almost one-line' scripts
* [[conversion between different image file formats]] - the ''convert'' command
* [[removing an excessive number of files from a directory - when 'rm' just isn't enough]]

===Cluster queues===
* [[submitting jobs, interactively or to a cluster queue system]]
* [[identifying job on a node]] - if you need to kill only one of few running jobs
* [[getting started with SLURM]]
* [[a guide to using SLURM to run PATHSAMPLE]]
* [[a guide to using SLURM to run GPU jobs on pat]]
* [[managing interactive jobs on cluster]]

===Miscellaneous/uncategorised===
* [[installing packages on your managed CUC3 workstation]]
* [[running programs in the background]] - so you can use your shell for other things at the same time
* [[finding bugs in latex documents that will not compile]]
* [[printing files from the command line using 'lpr']]
* [[uploading non image files to the wiki]]

== Compiler Flags ==

* [[Compiler Flags]]
* [[Blacklisting Compilers]]
* [[Lapack compilation]]
* [[Pdb to movie.py]]
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

== SuSE ==

* [[Upgrading destiny]]
* [[Upgrading sword]]
* [[SuSE 10.1 workstation image]]
* [[SuSE 10.2 workstation image]]
* [[SuSE 10.3 workstation image]]
* [[SuSE 11.1]]

--[[User:adk44|adk44]] 17.00, 9 May 2019 (BST)

AMBER

2021-10-07T16:00:06Z

Nn320: /* Tutorials */

'''[[Notes on AMBER 12 interface]]'''

[[Image:Amberpic.jpg|thumb|"The bugs have magically disappeared!"|200px|right]]
[http://amber.scripps.edu/ "AMBER"] (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. We mainly use the MM forcefields interfaced with other group software i.e. [[GMIN]] or [[OPTIM]]. The included programmes such as ''sander'' and ''antechamber'' are however, extremely useful in some circumstances! The full user manual for AMBER9 can be found in pdf format [http://amber.scripps.edu/doc9/amber9.pdf here].

As of July 2009, the SVN repository also contains AMBER Tools, the stand alone suite of programs that generate AMBER input files and allow you to analyse output. You can find a manual within the repository. Look in AMBERTOOLS/doc.

== Tutorials ==

* [[Using AMBER 14 on the GPU and compute clusters]]
* [http://amber.scripps.edu/tutorials/ Ross Walker's AMBER9 tutorials] - recommended reading for '''ANYONE''' using AMBER!
* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
* [[Generating parameters using RESP charges from GAMESS-US]]
* [[Simple scripts for LEaP to create topology and coordinate files]]
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide
* [[Symmetrising AMBER topology files]] - step by step guide for symmetrising a complex protein+ligand system
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb''
* [[Running GMIN with MD move steps AMBER]]
* [[Evaluating different components of AMBER energy function with SANDER]]
* [[Running MD with AMBER]]
* [[Running MD on GPUS with pmemd_cuda]]
* [[REMD with AMBER]]
* [[Performing a hydrogen-bond analysis]]

Preparing input files for a peptide using AMBER

2021-10-07T15:56:31Z

Nn320: Created page with "How to create input files for a peptide for use with GMIN? The steps given below are when you are trying to use one of the AMBER force fields. Step 0: Having amber on your s..."

How to create input files for a peptide for use with GMIN?
The steps given below are when you are trying to use one of the AMBER force fields.

Step 0: Having amber on your system

Assuming you have AMBER in your path by having something similar to this in ~/.bashrc
export AMBERHOME=/home/nn320/amber14
export PATH=$PATH:$AMBERHOME/bin
export PATH

Then run, `source ~/.bashrc` in the command line
Now you can run tleap from anywhere on your system

Step 1: Make topology and coordinates file using tleap in AMBER.

Run, `tleap -f leap.in`
leap.in file specifies force field, sequence, solvent model
My leap.in file has the following lines.

source leaprc.ff99SBildn
mol = sequence {ACE TYR TYR GLY GLY TYR TYR NME}
set default PBradii mbondi3
saveamberparm mol old_coords.prmtop coords.inpcrd
savepdb mol mol.pdb
quit

This gives a pdb, prmtop and incprd files as output
Note that pdb when visualised in vmd may have strange bonds.
This just means you need to minimise the structure to get proper geometry later.
Minimise the structure using sander in AMBER after
you have checked that library files used for creating coords.prmtop file are correct.

Step 2: Check the amber library files

After running tleap, make a note of all the library files that get loaded.
For example, in the above case,
all_nucleic94, all_amino94ildn, all_aminoct94ildn, all_aminont94ildn, ions94, solvents.lib
Check these library files with the ones given in softwarewales/AMBERTOOLS/dat/leap/lib
The amber14/dat/leap/lib library files for ff99SBildn are correct
This checking is necessary,
since the lib files for ff99SB i.e., all_aminoct94.lib have different charges for symmetrical atoms.
Basically, they differ in the following lines,
!entry.NHE.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 0 0 0 0 0
softwareWales ambertools> 1 1 0 0 0 0
!entry.NME.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
1 0 0 0 0 0
softwareWales ambertools> 1 3 0 0 0 0

In case the library files in amber are already correct, proceed to Step 3. If not,
make a copy of amber lib files somewhere and replace them with the ones in softwarewales/AMBERTOOLS
Repeat Step 1 i.e., use tleap again and create new coords.prmtop and coords.inpcrd file.

Step 3: Minimising the structure using sander

This is to ensure that coordinate file has a physical structure without atom overlaps.
For running sander, you just require, coords.prmtop, coords.inpcrd, min.in file
min.in file can have something like,
Minimization
&cntrl
imin = 1,
ncyc = 1000,
maxcyc = 2000,
igb=8, saltcon=0.1,
ntb = 0,
ntpr=100,
cut = 999.0,
rgbmax = 25.0
/

Then on the command line run,
$AMBERHOME/bin/sander -O -i min.in -o min.out -p coords.prmtop -c coords.inpcrd -r min.ncrst
The min.ncrst has minimised geometry.
To visualise it and compare it with initial geometry run the following,
$AMBERHOME/bin/ambpdb -p coords.prmtop -c min.ncrst > minncrst.pdb
To visualise older coords.inpcrd, just use the above command replacing coordinate file and the output file.

Use the min.ncrst so obtained as your new coords.inpcrd file.
So, now you have obtained your coords.prmtop and coords.inpcrd file using AMBER.

Step 4: Symmetrise the topology file so obtained

Symmetrisation scripts are given in ~/softwarewales/SCRIPTS/AMBER/symmetrise_prmtop/
For the above force field use perm-prmtop.py script. It is written in python2.
Its usage is
perm-prmtop.py old.prmtop symmetrised.prmtop

You do want to check whether your topology file is symmetrised properly.
Basically, symmetrisation means that when you permute the permutable atoms in your system
the energy should not change
The best way to check correct symmetrisation is by first creating perm.allow file
and then generating several coords.inpcrd files
and calculating single point energy of each of them to get the same energy.

Step 5: Creating a perm.allow file

Run `perm-pdb.py name.pdb AMBER`
The perm-pdb.py is a python2 script found in ~/softwarewales/SCRIPTS/make_perm.allow/

To check the perm.allow file simply read the documentation of PERMDIST
and check the atom numbers in perm.allow with the atom numbers using vmd or pymol
and check yourself if those atom numbers correspond to permutable atoms.

Step 6: Check symmetrisation

Step 6a: Creation of several coords.inpcrd files with permuted atoms
Step 6b: Run GMIN or A12GMIN in this case to check if their energies are the same.

Of course, you would want this process to be automated. The script I used can be found
on sinister in /home/nn320/bin/symm_check.sh

You can probably stop here, you have coords.prmtop and coords.inpcrd file for your peptide using ff99SBildn force field.

Step 7: Creating topology file for modified force field ff99IDPs

Since we want to use a modified force field ff99IDPs (https://github.com/chaohao2010/ADD-CMAP)
Follow the steps given on the website
You may have to make the python files executable
chmod 755 ADD_CMAP.py
Obtain another prmtop file
This should already be symmetrised
The command to use is, you will have to unload python2 and load python3 module.
python3 ADD-CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s
or
python3 ADD_CMAP.py -p amber.prmtop -c ff99IDPs.para -o amber_CMAP.prmtop -s
Here, amber.prmtop represents the symmetrised prmtop and amber_CMAP.prmtop
is the new coords.prmtop for ff99IDPs force field.
These files ADD_CMAP.py and ff99IDPs.para can be found on sinister in
/home/nn320/ff99idps_files
You might like to check two things
a) Symmetrisation of this new topology file by repeating the step 6
b) Whether the A12GMIN and GMIN energy for a structure agree with each other.

Step 8: Creating atomgroups file

To create atomgroups file, have a look at http://www-wales.ch.cam.ac.uk/examples/GMIN/1LE0/
and write it yourself

Note: Input files you should have for your peptide system to use with GMIN, OPTIM, PATHSAMPLE

coords.prmtop, coords.inpcrd, atomgroups, perm.allow, min.in, data
min.in file can have
Minimization
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 8, saltcon=0.1,
ntb = 0,
cut = 999.0,
rgbmax = 25.0
/

Example data file can be
TEMPERATURE 0.5962
SLOPPYCONV 1.0D-4
TIGHTCONV 1.0D-7
MAXERISE 1.0D-4
TRACKDATA
ACCEPTRATIO 0.2
DUMPINT 100
UPDATES 1500
MAXIT 3000 5000
MAXBFGS 0.2D0
STEPS 1 1.0
STEP 0.0 0.0
DEBUG
RADIUS 1000.0
ENERGY_DECOMP
AMBER12

Miscellaneous

PLEASE PLEASE NOTE THAT SCEE values are 1.2 and SCNB values are 2.0 for AMBER. Check AMBER manual for more information.
The topology files created using above method have 0.0 for improper torsions. The program should not try to invert these zeros.
There was a bug in AMBER12 which has been corrected in AMBER20. So do not worry about SCEE and SCNB now.

AMBER

2021-10-07T15:51:46Z

Nn320: /* Tutorials */

'''[[Notes on AMBER 12 interface]]'''

[[Image:Amberpic.jpg|thumb|"The bugs have magically disappeared!"|200px|right]]
[http://amber.scripps.edu/ "AMBER"] (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. We mainly use the MM forcefields interfaced with other group software i.e. [[GMIN]] or [[OPTIM]]. The included programmes such as ''sander'' and ''antechamber'' are however, extremely useful in some circumstances! The full user manual for AMBER9 can be found in pdf format [http://amber.scripps.edu/doc9/amber9.pdf here].

As of July 2009, the SVN repository also contains AMBER Tools, the stand alone suite of programs that generate AMBER input files and allow you to analyse output. You can find a manual within the repository. Look in AMBERTOOLS/doc.

== Tutorials ==

* [[Using AMBER 14 on the GPU and compute clusters]]
* [http://amber.scripps.edu/tutorials/ Ross Walker's AMBER9 tutorials] - recommended reading for '''ANYONE''' using AMBER!
* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
* [[Generating parameters using RESP charges from GAMESS-US]]
* [[Simple scripts for LEaP to create topology and coordinate files]]
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
* [[Preparing input files for a peptide using AMBER]] - detailed guide
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide
* [[Symmetrising AMBER topology files]] - step by step guide for symmetrising a complex protein+ligand system
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb''
* [[Running GMIN with MD move steps AMBER]]
* [[Evaluating different components of AMBER energy function with SANDER]]
* [[Running MD with AMBER]]
* [[Running MD on GPUS with pmemd_cuda]]
* [[REMD with AMBER]]
* [[Performing a hydrogen-bond analysis]]

Symmetrising AMBER topology files

2021-09-17T13:23:34Z

Nn320:

== Symmetrising a Simple Protein System ==

=== The Basics ===

When LEap is used to generate AMBER topology files ('''coords.prmtop''') it doesn't do a very good job of ensuring that improper dihedral angle energies are invariant with respect to permutations.

These energies can be made invariant by rearranging the permutable atoms within the relevant dihedral term in the '''coords.prmtop''' file. For example, the residue aspartate has two permutable oxygen atoms (described by OD1 and OD2 respectively, with the relevant dihedral angle also including two carbon atoms, CB and CG). The dihedral describing these atoms is typically represented in '''coords.prmtop''' as CB-OD1-CG-OD2. In order to symmetrise these oxygen atoms, this must be rearranged to OD1-CB-CG-OD2 (i.e. the first permutable atom must be listed first in the dihedral, and the second permutable atom listed fourth). The reasons for this are somewhat esoteric but the paper [https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21425 here] addresses it rather well.

The %FLAG DIHEDRALS_INC_HYDROGEN and %FLAG DIHEDRALS_WITHOUT_HYDROGEN sections in '''coords.prmtop''' list the groups of dihedrals present in your system. Strangely, these are listed not in terms of atomic indices but instead in terms of the atomic index multiplied by 3, with 1 then subtracted. You can probably imagine that trying to find all of the relevant permutable atoms to swap in the '''coords.prmtop''' file (which can be quite a lot in a protein system!) can become very tedious indeed, if done manually.

Fortunately, scripts have been written ('''perm-prmtop.*.py''', which can be found in ~/svn/SCRIPTS/AMBER/symmetrise_prmtop) that can identify these atoms within the dihedral terms that need to be swapped, and then does it for you.

Note that the 1-4 non-bonded interactions are not calculated for improper torsions to avoid double counting. The double counting can be understood by considering a torsion 1-2-3-4 as a normal one and 1-3-2-4 as improper torsion. Improper torsions are designed to keep atoms in a plane. In the AMBER topology file, the dihedrals are defined such that the actual atom index A =N/3 +1 where N is the absolute value of coordinate array index (http://ambermd.org/prmtop.pdf).

=== Ensuring the termini are correct ===

The python scripts mentioned above only work if the termini of your protein system are properly considered. This is because the improper dihedrals for terminal residues are different.

It is possible to alter the '''coords.prmtop''' file manually to account for these termini. First, find the section of your file formatted as follows:
<pre>
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ALA GLU PHE
%FLAG RESIDUE_POINTER
</pre>

The chances are that your protein system will be much bigger and contain many more residues but the principles are the same. Each residue technically is assigned four spaces, although one of these is usually blank. This is no longer the case when the terminal residues are altered to reflect whether they are N-terminal or C-terminal. In this case, ALA is transformed to NALA and PHE to CPHE. This gives:
<pre>
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
NALAGLU CPHE
%FLAG RESIDUE_POINTER
</pre>

There is a script, '''A9prmtoptermini.sh''' (which can also be found in ~/svn/SCRIPTS/AMBER/symmetrise_prmtop), which does this for you. A typical command would be something like this:

./A9prmtoptermini.sh initial.prmtop final.prmtop initial.pdb ff02

Please note that to run this script, you need a .pdb file as well as a .prmtop file. ff02 specifies which [[AMBER]] forcefield to use (and therefore which of the perm-prmtop.*.py files to select).

== Symmetrising a Protein System with Cofactors ==

=== Including these cofactors in the first place ===

The method above works if your system comprises only protein residues. However, you may be interested in how a certain molecule or group of molecules interacts with the protein. The addition of these cofactors presents many challenges. If your cofactor is very unusual, you may even need to generate parameters yourself. In which case, it may be useful to refer to some of the [[AMBER]] tutorials, such as this one [http://ambermd.org/tutorials/advanced/tutorial1/index.htm here]. Fortunately, many of the most-commonly used cofactors have already been parameterised, particularly by the [http://research.bmh.manchester.ac.uk/bryce/amber Bryce Group] in Manchester.

There is already a page, [[Setting up]], which deals quite comprehensively in how to generate [[AMBER]] input files using LEap. When you want to include cofactors in your system, all you have to do is ensure that the relevant .frcmod and .prepin (or .lib) files are included when you use tleap or xleap. It's also useful to have a .pdb file from another database or source (such as from an X-ray crystallography structure on the [https://www.rcsb.org/ Protein Data Bank]), although this is not strictly necessary. These files may not be formatted in an appropriate way (again, for details, see [[Setting up]]).

Below is an example. After launching tleap, and ensuring all of the relevant files were in my PATH or working directory, I generated a set of [[AMBER]] input files for a protein called HemS alongside haem and NADH cofactors ''via'' the following commands:
<pre>
source leaprc.ff99SB
loadamberparams hem.frcmod
loadamberprep hem.prepin
loadoff nadh.lib
loadamberparams nadh.frcmod
mol=loadpdb 1.pdb
savepdb mol start.pdb
saveamberparm mol coords.prmtop.old coords.inpcrd
</pre>

=== Symmetrising the cofactors as well as the residues ===

Of course, this creates [[AMBER]] input files where the permutable atoms aren't necessarily properly symmetrised. Depending upon what cofactors you're including, these could contain permutable atoms as well. Therefore, we must ensure that when finding the correct symmetry, we include the relevant cofactor libraries too or else only the atoms in the standard residues will be treated.

A four-point plan to deal with protein systems containing cofactors that need symmetrising is as follows:

1.
* First, make sure the cofactors in you system are already listed in perm-prmtop.*.py.
* To do this: grep -r 'group8 =' .
* This should give a list of all of the cofactors contained in the various perm-prmtop files (perm-prmtop.ff02.py, perm-prmtop.ff03.py and perm-prmtop.ff14.py should have identical lists).
* If your cofactor is present, proceed to step 2.
* If it's not present, you will have to insert the relevant library for your cofactor, and list which atoms need to be symmetrised. Please do this for perm-prmtop.ff02.py, perm-prmtop.ff03.py and perm-prmtop.ff14.py in order to keep them consistent (this should be a simple copy and paste job). Also, it would be helpful once you've done this if you add your new cofactor to the group8 list.

2.
* Ensure that your relevant cofactor libraries are in your working directory, e.g. if the cofactors in your system are haem (HEM) and NADH (NAD), make sure that hem.lib and nadh.lib are present.

3.
* Make a note of the first atom in each of your cofactors. This corresponds to the third column in your pdb file. Using HEM and NAD again as examples, the first atoms for each are FE and P1 respectively.

4.
* Now we have all of the information we need to launch our symmetrisation. Just add on the atoms you noted in step 3 as extra arguments, e.g.
** ./A9prmtoptermini.sh initial.prmtop final.prmtop initial.pdb ff02 FE P1

And behold, your system is properly symmetrised. The natural order of things, alongside Rangers beating Celtic in the Old Firm or Scotland thumping England in the Rugby, is returned to the universe. You are now ready to launch your [[GMIN]] or [[OPTIM]] calculations.

--adk44 17.00, 9 May 2019 (BST)

Compiling Wales Group codes using cmake

2021-07-22T14:13:55Z

Nn320:

[http://www.cmake.org/ CMake] (Cross-platform Make) provides a simple, platform independent way for us to compile and test the group codebase. Dependencies are handled automatically, compilation can proceed in parallel to avoid long waits while testing changes and builds are done entirely outside of the source directory. It also enables us to use the [[Jenkins CI]] 'build bot' system to automatically compile and test the code on a nightly basis - helping us catch troublesome commits before they affect other users.

Although everything below refers to compiling [[GMIN]] with the Intel ''ifort'' compiler and AMBER9 - the exact same procedure works for [[OPTIM]] and [[PATHSAMPLE]].

Note that not every option for our codes is expected to actually compile with every compiler, for example, anything using CHARMM35/36 will not compile with ''nagfor'' or ''gfortran''. This is nothing to do with our code - it's a CHARMM issue. You can get an idea for what should work by looking at the automated [[Jenkins CI]] builds.

==Preparing to compile==
Before you get started, you need to ensure that the machine you are planning to compile on has cmake 2.8 or higher installed. You can check the current version like so:
<pre>
cmake --version
</pre>

The clusters have a module for cmake 3.0, which you can load using the following command:
<pre>
module load cmake/3.0.0
</pre>

You also need to create a directory to build the code in. We suggest that you create a directory for the compiler you are using within the program directory, under a subdirectory called 'builds' - for example for compiling GMIN with ifort, you would make a directory here:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/ifort
cd ~/softwarewales/GMIN/builds/ifort
</pre>
You can call these directories whatever you like - but make sure it is clear to you what they contain! You might also want to check which version of the compiler you have loaded. This is important as the different clusters and workstations may have different default versions loaded, some of which might not work properly. You can check the compiler version currently loaded using the same '--version' flag we used for ''cmake'' above:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ifort --version
ifort (IFORT) 12.1.3 20120212
Copyright (C) 1985-2012 Intel Corporation. All rights reserved.
</pre>

To load a different compiler, you can use the ''module load'' or ''module swap'' commands. A list of all available modules can be accessed using:
<pre>
module av
</pre>
If you are having problems compiling, one of the first things to check is whether it works with a different version of the compiler!

'''Note: When compiling GMIN, if you are getting the error that there is no implicit type for ERFC in ewald.f90, try using a newer version of your compiler. This should be the built-in complementary error function.'''

==Compiling using the ccmake GUI interface to set options==
[[Image:Ccmake.png|thumb|ccmake set up to compile A9GMIN|200px|right]]

One advantage using cmake has over make is that we can use the simple ccmake GUI. This interface lets us set options like compiling with AMBER9, or CHARMM35, toggle between 'Release' and 'Debug' builds (see below) - and examine and alter the flags being uses for the compilation if we wish. Before we can run ccmake, we need to specify the compiler and run cmake in our build directory (e.g. softwarewales/GMIN/builds/ifort). We specify the '''F'''ortran '''C'''ompiler by setting the '''$FC''' environment variable (in this case the Intel Fortran compiler, ifort), and then run ''cmake'' (on the command line), passing it the relative location of the [[GMIN]] source directory:
<pre>
FC=ifort cmake ../../source
</pre>

If you run ''ls'', you will see some cmake files have been generated:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ls
CMakeCache.txt CMakeFiles cmake_install.cmake Makefile modules
</pre>

You can now run ''ccmake'' to open the GUI:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ccmake .
</pre>

To navigate between options, use the arrow keys. Options can be toggled by pressing Return. To compile [[GMIN]] with AMBER9 (A9GMIN), we need to toggle the ''WITH_AMBER'' option ''ON''. Once you have done this, you need to configure and generate appropriate cmake info. This is done by pressing 'c' to configure, 'e' to exit and then 'g' to generate.

'''Note: for some builds (CHARMM with DFTB and CUDAGMIN), you might need to configure, exit and generate twice to set all necessary options'''

You can now compile A9GMIN in parallel as follows:
<pre>
make -j8
</pre>

The '-j8' flag here tells make to use up to 8 'threads' when building. For optimal performance, you should keep this slightly greater than the number of cores (CPUs) the node you are working on has. If all goes well, you should now have an A9GMIN binary in your build directory - congratulations!
<pre>
Linking Fortran executable A9GMIN
[100%] Built target A9GMIN

--------------------------------------------------------------------------------------------- 15:23:45

csw34@sinister:~/softwarewales/GMIN/builds/ifort> ls
A9GMIN cmake_install.cmake libcudadummylib.a libmylapack.a NAB
AMBER display_version.f90 libdummylib.a Makefile nab_binaries_built
CMakeCache.txt GMIN libgminlib.a modules porfuncs.f90
CMakeFiles libamber12dummylib.a libmyblas.a n
</pre>
Plain [[GMIN]] is also built at the same time should you need it. You can move this into your ~/bin directory if you like, or anywhere else in your ''$PATH'' to make running it simple.

'''Note: If you want to use OPTIM with the new C++ implementation of the NEB routine, you will need to obtain the source code for that separately. See [https://wikis.ch.cam.ac.uk/wales/wiki/index.php/OPTIM here] for instructions.'''

==Compiling by setting options on the command line==
If you know the options you'd like to set already (you can see them all in ccmake), you can save some time by passing them directly to ''cmake'' on the command line, bypassing the need for ''ccmake''. For example, to compile A9GMIN (GMIN with the AMBER9 interface) using the Intel ifort compiler, you would run the following commands:
<pre>
FC=ifort cmake -DWITH_AMBER=1 ../../source
make -j8
</pre>
where '../../source' is the relative location of the GMIN source directory. You can find some more examples of compiling from the command line below.

'''Note: Sometimes you may get error''' (for example, Fatal Error: Can't open module file 'someModule.mod' for reading at (1): No such file or directory) when following this procedure. In that case there are three things you could try: make sure you are building in a new directory, if that does not help run `make VERBOSE=1` instead of `make -j8` or simply switch to using ccmake.

==Compiling with MPI==
To compile with MPI support add the following flags when running cmake on the command line:
<pre>
FC=mpif90 CC=mpicc cmake ../source -DCOMPILER_SWITCH=pgi -DWITH_MPI=yes
</pre>
Here -DCOMPILER_SWITCH=pgi assumes you're using the Portland ''pgi'' compiler. Make sure you have the correct modules loaded (in this case ''pgi'' and ''mpi-pgi''), and that the particular mpi you want (in this case ''mpi-pgi'') is listed before any other mpi's loaded (so that it has the highest priority). The modules can be loaded by typing:
<pre>
module load pgi/64/
module load mpi/openmpi/pgi/64/1.6.3
</pre>

and you can check which modules are loaded and in which order/priority by the ''module list'' command. You may need to ''module unload <name>'' any other mpi's that are higher up in the list than the one you want. You can of course set the COMPILER_SWITCH and WITH_MPI flags in ''ccmake'' if you prefer.

Note: It has been observed that pgi/64/15.1 leads to compilation errors, and for now, it is best to use pgi/64/14.9

==Advanced mode - changing compiler flags with ccmake==
[[Image:Ccmakeadvanced.png|thumb|ccmake advanced mode|200px|right]]

Although initially the ''ccmake'' GUI looks very simple, there is a lot going on under the hood. By pressing 't' you can enter 'Advanced mode' which will show you all of the hidden options, for example the compiler flags that are being passed to ''make'' when you compile the code. You can also make changes to the flags here, for example if you would like to add '-p' to do profiling.

As with changing the build type, you simply select the field you'd like to change using the arrow keys, press Return, make your changes and press Return again to save them. When you subsequently configure and generate as above, those altered flag will be used for the subsequent compilation.

Note that these changes only apply in the build directory in which you make them.

==Debugging runtime problems using gdb or valgrind==
If you are getting a segmentation fault, crash or other unexpected behaviour, you might want to run your job through a debugger like [http://www.gnu.org/software/gdb/ gdb] or [http://valgrind.org/ valgrind]. In order to maximise your chances of getting useful output, you should build a 'Debug' version of the program you are having trouble. To do this, you can either change the ''CMAKE_BUILD_TYPE'' in ''ccmake'' to 'Debug' (press Return, change 'Release' to 'Debug' and press Return again), or on the command line like so for GMIN with AMBER 9 using the Intel ifort compiler:
<pre>
FC=ifort cmake -DCMAKE_BUILD_TYPE=Debug -DWITH_AMBER=1 ../../source
make -j8
</pre>

You can then run the binary ''through'' gdb or valgrind as follows:
<pre>
gdb A9GMIN
</pre>
or
<pre>
valgrind A9GMIN
</pre>

I won't cover debugging with these tools here as it's a science in itself! Do some Googling and ask for help as needed :)

==Debugging compilation problems==
There are many ways to try and track down why your code is not compiling. Before you start changing compilers, building a 'Debug' version or changing machines, you might want to try running make again with the ''VERBOSE'' option enabled. This will dump a lot of potentially useful output:
<pre>
VERBOSE=1 make
</pre>

One possible gotcha: all .f and .f90 files in the relevant source directories will be compiled and added to a library. This is quite different from the old Makefile way of doing things, where source files were explicitly specified for compilation (via their corresponding .o file). So, if you are testing something by for instance copying code.f90 to code.myhack.f90 and code.orig.f90, then slightly editing a line or two of code.myhack.f90 and copying it back to code.f90 for use, this will probably cause linking problems due to multiply-defined subroutines (from all three files). The solution, if you must have alternative versions of the same file hanging round, is to differentiate the filenames by a suffix AFTER the .f[90] .

Another occasional issue is the unexplained compiler bug - a problem with the version of the compiler you happen to be using. You can can an idea for which compiler versions we expect to work by checking the Jenkins build-bot output, as described in the 'Seeing console output' section of the [[Jenkins CI]] page. If you are using a different version of the compiler in question, consider swapping to the version Jenkins is using with 'module swap'.

If the error message you are getting doesn't make sense to you after some Googling, go and ask someone - we all have these problems. Things you can try first include trying a different compiler version, or an entirely different compiler e.g. pgi rather than ifort for example. You should bear in mind that as mentioned above, not all versions of each code will compile with every compiler. Make sure you're not trying to build something that isn't expected to work.

==Extra command line build examples==
The below commands are absolutely not an exhaustive list, but should give you an idea of what is possible. You can use ''ccmake'' as described above to discover which variables (e.g. WITH_AMBER) can be manipulated on the command line like this. All of these examples assume your svn repository is set up in ''/home/CRSID/svn'' - make the appropriate modifications if you have it elsewhere.

===GMIN===
'''A12GMIN''' (GMIN with AMBER12) using ifort:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/ifort_amber12
cd !$
FC=ifort cmake -DWITH_AMBER12=1 ../../source
make -j8
</pre>

'''C35GMIN''' (GMIN with CHARMM 35) using pgi:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/pgi_charmm35
cd !$
FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source
make -j8
</pre>

'''CUDAGMIN''' (GMIN leveraging GPU minimisation via the AMBER 12 interface) using ifort:
<pre>
module load cuda/5.5
mkdir -p ~/softwarewales/GMIN/builds/ifort_cuda
cd !$
FC=ifort cmake -DWITH_CUDA=1 ../../source
make -j8
</pre>
This will only work on machines with specific NVIDIA GPUs, for example when submitting jobs on the pat cluster. There is some additional information on the [[Using GMIN with GPUs]] page.

===OPTIM===
'''A9OPTIM''' (OPTIM with AMBER9) using ifort:
<pre>
mkdir -p ~/softwarewales/OPTIM/builds/ifort_amber
cd !$
FC=ifort cmake -DWITH_AMBER9=1 ../../source
make -j8
</pre>

'''C35OPTIM''' (OPTIM with CHARMM 35) using pgi:
<pre>
mkdir -p ~/softwarewales/OPTIM/builds/pgi_charmm35
cd !$
FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source
make -j8
</pre>

'''CUDAOPTIM''' (OPTIM leveraging GPU via the AMBER 12 interface) using ifort:
<pre>
module load cuda/5.5
mkdir -p ~/softwarewales/OPTIM/builds/ifort_cuda5.5
cd !$
FC=ifort CC=icc cmake -DWITH_CUDA=1 ../../source
make -j8
</pre>
This will only work on machines with specific NVIDIA GPUs, for example when submitting jobs on the pat cluster. There is some additional information on the [[Using GMIN and OPTIM with GPUs]] page.

===PATHSAMPLE===
There are very few options for [[PATHSAMPLE]] as we don't need to worry about interfacing with a particular potential. As a result, every binary is simply called ''PATHSAMPLE''.

Using nagfor (the NAG fortran compiler - check you have the module loaded - very strict!):
<pre>
mkdir -p ~/softwarewales/PATHSAMPLE/builds/nagfor
cd !$
FC=nagfor cmake ../../source
make -j8
</pre>

Using pgi (much more generous with coding slips/non-standard uses):
<pre>
mkdir -p ~/softwarewales/PATHSAMPLE/builds/pgi
cd !$
FC=pgf90 cmake ../../source
make -j8
</pre>

==Configuring defaults - for developers==

Fortran compilers and their corresponding default settings are all controlled by the file $SVN/CMakeModules/FindFORTRANCOMPILER.cmake ($SVN is your svn root directory). In particular, we may wish to edit the flags used for each set of compilers and build type. These are contained in the following block:

<pre>
if(NOT COMPILER_FLAGS_WERE_SET)
message("Setting initial values for compiler flags")
if(COMPILER_SWITCH MATCHES "pgi")
set (CMAKE_Fortran_FLAGS "-Mextend" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -Munroll -Mnoframe" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-Mextend -C -g -gopt -Mbounds -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -Mdwarf1 -Mdwarf2 -Melf -Mpgicoff -traceback" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-Mextend -C -g -gopt -Mbounds -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -Mdwarf1 -Mdwarf2 -Mdwarf3 -Melf -Mpgicoff -traceback" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-Mfree" CACHE TYPE STRING)
elseif(COMPILER_SWITCH MATCHES "gfortran")
set (CMAKE_Fortran_FLAGS "-ffixed-line-length-200 -ffree-line-length-0" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE TYPE STRING FORCE)
# set (CMAKE_Fortran_FLAGS_DEBUG "-g -fbounds-check -Wuninitialized -O -ftrapv -fimplicit-none -fno-automatic" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-g -fbounds-check -Wuninitialized -O -ftrapv -fno-automatic" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "${CMAKE_Fortran_FLAGS_DEBUG} -fimplicit-none" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-ffree-form" CACHE TYPE STRING)
elseif(COMPILER_SWITCH MATCHES "nag")
set (CMAKE_Fortran_FLAGS "-132 -kind=byte -maxcontin=3000" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-mismatch_all -O4" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-g -mismatch_all -ieee=stop" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-C=all -mtrace=all -gline -g -mismatch_all -ieee=stop" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-free" CACHE TYPE STRING) # js850> is this ever used?
elseif(COMPILER_SWITCH MATCHES "ifort")
set (CMAKE_Fortran_FLAGS "-132 -heap-arrays -assume byterecl" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE TYPE STRING FORCE)
# Warnings about temporary argument creation and edit descriptor widths are disabled with the final flags.
set (CMAKE_Fortran_FLAGS_DEBUG "-C -g -traceback -debug full -check all,noarg_temp_created -diag-disable 8290,8291" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-debug all -check all -implicitnone -warn unused -fp-stack-check -ftrapuv -check pointers -check bounds" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-free" CACHE TYPE STRING)
else()
message(FATAL_ERROR "unknown comiler switch: ${COMPILER_SWITCH}")
endif()
SET(COMPILER_FLAGS_WERE_SET yes CACHE TYPE INTERNAL)
endif(NOT COMPILER_FLAGS_WERE_SET)
</pre>

The main if/elseif blocks correspond to compiler switches. Inside these, there are the default flags for each of our build types (release, debug and debug_slow), which are configured using ccmake. These can be edited, if we wish to change the default behaviour (e.g. a recent addition of -check all,noarg_temp_created -diag-disable 8290,8291 to disable annoying warning messages for ifort).

Compiling Wales Group codes using cmake

2021-07-22T14:12:13Z

Nn320:

[http://www.cmake.org/ CMake] (Cross-platform Make) provides a simple, platform independent way for us to compile and test the group codebase. Dependencies are handled automatically, compilation can proceed in parallel to avoid long waits while testing changes and builds are done entirely outside of the source directory. It also enables us to use the [[Jenkins CI]] 'build bot' system to automatically compile and test the code on a nightly basis - helping us catch troublesome commits before they affect other users.

Although everything below refers to compiling [[GMIN]] with the Intel ''ifort'' compiler and AMBER9 - the exact same procedure works for [[OPTIM]] and [[PATHSAMPLE]].

Note that not every option for our codes is expected to actually compile with every compiler, for example, anything using CHARMM35/36 will not compile with ''nagfor'' or ''gfortran''. This is nothing to do with our code - it's a CHARMM issue. You can get an idea for what should work by looking at the automated [[Jenkins CI]] builds.

==Preparing to compile==
Before you get started, you need to ensure that the machine you are planning to compile on has cmake 2.8 or higher installed. You can check the current version like so:
<pre>
cmake --version
</pre>

The clusters have a module for cmake 3.0, which you can load using the following command:
<pre>
module load cmake/3.0.0
</pre>

You also need to create a directory to build the code in. We suggest that you create a directory for the compiler you are using within the program directory, under a subdirectory called 'builds' - for example for compiling GMIN with ifort, you would make a directory here:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/ifort
cd ~/softwarewales/GMIN/builds/ifort
</pre>
You can call these directories whatever you like - but make sure it is clear to you what they contain! You might also want to check which version of the compiler you have loaded. This is important as the different clusters and workstations may have different default versions loaded, some of which might not work properly. You can check the compiler version currently loaded using the same '--version' flag we used for ''cmake'' above:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ifort --version
ifort (IFORT) 12.1.3 20120212
Copyright (C) 1985-2012 Intel Corporation. All rights reserved.
</pre>

To load a different compiler, you can use the ''module load'' or ''module swap'' commands. A list of all available modules can be accessed using:
<pre>
module av
</pre>
If you are having problems compiling, one of the first things to check is whether it works with a different version of the compiler!

'''Note: When compiling GMIN, if you are getting the error that there is no implicit type for ERFC in ewald.f90, try using a newer version of your compiler. This should be the built-in complementary error function.'''

==Compiling using the ccmake GUI interface to set options==
[[Image:Ccmake.png|thumb|ccmake set up to compile A9GMIN|200px|right]]

One advantage using cmake has over make is that we can use the simple ccmake GUI. This interface lets us set options like compiling with AMBER9, or CHARMM35, toggle between 'Release' and 'Debug' builds (see below) - and examine and alter the flags being uses for the compilation if we wish. Before we can run ccmake, we need to specify the compiler and run cmake in our build directory (e.g. softwarewales/GMIN/builds/ifort). We specify the '''F'''ortran '''C'''ompiler by setting the '''$FC''' environment variable (in this case the Intel Fortran compiler, ifort), and then run ''cmake'' (on the command line), passing it the relative location of the [[GMIN]] source directory:
<pre>
FC=ifort cmake ../../source
</pre>

If you run ''ls'', you will see some cmake files have been generated:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ls
CMakeCache.txt CMakeFiles cmake_install.cmake Makefile modules
</pre>

You can now run ''ccmake'' to open the GUI:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ccmake .
</pre>

To navigate between options, use the arrow keys. Options can be toggled by pressing Return. To compile [[GMIN]] with AMBER9 (A9GMIN), we need to toggle the ''WITH_AMBER'' option ''ON''. Once you have done this, you need to configure and generate appropriate cmake info. This is done by pressing 'c' to configure, 'e' to exit and then 'g' to generate.

'''Note: for some builds (CHARMM with DFTB and CUDAGMIN), you might need to configure, exit and generate twice to set all necessary options'''

You can now compile A9GMIN in parallel as follows:
<pre>
make -j8
</pre>

The '-j8' flag here tells make to use up to 8 'threads' when building. For optimal performance, you should keep this slightly greater than the number of cores (CPUs) the node you are working on has. If all goes well, you should now have an A9GMIN binary in your build directory - congratulations!
<pre>
Linking Fortran executable A9GMIN
[100%] Built target A9GMIN

--------------------------------------------------------------------------------------------- 15:23:45

csw34@sinister:~/softwarewales/GMIN/builds/ifort> ls
A9GMIN cmake_install.cmake libcudadummylib.a libmylapack.a NAB
AMBER display_version.f90 libdummylib.a Makefile nab_binaries_built
CMakeCache.txt GMIN libgminlib.a modules porfuncs.f90
CMakeFiles libamber12dummylib.a libmyblas.a n
</pre>
Plain [[GMIN]] is also built at the same time should you need it. You can move this into your ~/bin directory if you like, or anywhere else in your ''$PATH'' to make running it simple.

'''Note: If you want to use OPTIM with the new C++ implementation of the NEB routine, you will need to obtain the source code for that separately. See [https://wikis.ch.cam.ac.uk/wales/wiki/index.php/OPTIM here] for instructions.'''

==Compiling by setting options on the command line==
If you know the options you'd like to set already (you can see them all in ccmake), you can save some time by passing them directly to ''cmake'' on the command line, bypassing the need for ''ccmake''. For example, to compile A9GMIN (GMIN with the AMBER9 interface) using the Intel ifort compiler, you would run the following commands:
<pre>
FC=ifort cmake -DWITH_AMBER=1 ../../source
make -j8
</pre>
where '../../source' is the relative location of the GMIN source directory. You can find some more examples of compiling from the command line below.

'''Note: Sometimes you may get error''' (for example, Fatal Error: Can't open module file 'someModule.mod' for reading at (1): No such file or directory) when following this procedure. In that case there are three things you could try: make sure you are building in a new directory, if that does not help run `make VERBOSE=1` instead of make -j8 or simply switch to using ccmake.

==Compiling with MPI==
To compile with MPI support add the following flags when running cmake on the command line:
<pre>
FC=mpif90 CC=mpicc cmake ../source -DCOMPILER_SWITCH=pgi -DWITH_MPI=yes
</pre>
Here -DCOMPILER_SWITCH=pgi assumes you're using the Portland ''pgi'' compiler. Make sure you have the correct modules loaded (in this case ''pgi'' and ''mpi-pgi''), and that the particular mpi you want (in this case ''mpi-pgi'') is listed before any other mpi's loaded (so that it has the highest priority). The modules can be loaded by typing:
<pre>
module load pgi/64/
module load mpi/openmpi/pgi/64/1.6.3
</pre>

and you can check which modules are loaded and in which order/priority by the ''module list'' command. You may need to ''module unload <name>'' any other mpi's that are higher up in the list than the one you want. You can of course set the COMPILER_SWITCH and WITH_MPI flags in ''ccmake'' if you prefer.

Note: It has been observed that pgi/64/15.1 leads to compilation errors, and for now, it is best to use pgi/64/14.9

==Advanced mode - changing compiler flags with ccmake==
[[Image:Ccmakeadvanced.png|thumb|ccmake advanced mode|200px|right]]

Although initially the ''ccmake'' GUI looks very simple, there is a lot going on under the hood. By pressing 't' you can enter 'Advanced mode' which will show you all of the hidden options, for example the compiler flags that are being passed to ''make'' when you compile the code. You can also make changes to the flags here, for example if you would like to add '-p' to do profiling.

As with changing the build type, you simply select the field you'd like to change using the arrow keys, press Return, make your changes and press Return again to save them. When you subsequently configure and generate as above, those altered flag will be used for the subsequent compilation.

Note that these changes only apply in the build directory in which you make them.

==Debugging runtime problems using gdb or valgrind==
If you are getting a segmentation fault, crash or other unexpected behaviour, you might want to run your job through a debugger like [http://www.gnu.org/software/gdb/ gdb] or [http://valgrind.org/ valgrind]. In order to maximise your chances of getting useful output, you should build a 'Debug' version of the program you are having trouble. To do this, you can either change the ''CMAKE_BUILD_TYPE'' in ''ccmake'' to 'Debug' (press Return, change 'Release' to 'Debug' and press Return again), or on the command line like so for GMIN with AMBER 9 using the Intel ifort compiler:
<pre>
FC=ifort cmake -DCMAKE_BUILD_TYPE=Debug -DWITH_AMBER=1 ../../source
make -j8
</pre>

You can then run the binary ''through'' gdb or valgrind as follows:
<pre>
gdb A9GMIN
</pre>
or
<pre>
valgrind A9GMIN
</pre>

I won't cover debugging with these tools here as it's a science in itself! Do some Googling and ask for help as needed :)

==Debugging compilation problems==
There are many ways to try and track down why your code is not compiling. Before you start changing compilers, building a 'Debug' version or changing machines, you might want to try running make again with the ''VERBOSE'' option enabled. This will dump a lot of potentially useful output:
<pre>
VERBOSE=1 make
</pre>

One possible gotcha: all .f and .f90 files in the relevant source directories will be compiled and added to a library. This is quite different from the old Makefile way of doing things, where source files were explicitly specified for compilation (via their corresponding .o file). So, if you are testing something by for instance copying code.f90 to code.myhack.f90 and code.orig.f90, then slightly editing a line or two of code.myhack.f90 and copying it back to code.f90 for use, this will probably cause linking problems due to multiply-defined subroutines (from all three files). The solution, if you must have alternative versions of the same file hanging round, is to differentiate the filenames by a suffix AFTER the .f[90] .

Another occasional issue is the unexplained compiler bug - a problem with the version of the compiler you happen to be using. You can can an idea for which compiler versions we expect to work by checking the Jenkins build-bot output, as described in the 'Seeing console output' section of the [[Jenkins CI]] page. If you are using a different version of the compiler in question, consider swapping to the version Jenkins is using with 'module swap'.

If the error message you are getting doesn't make sense to you after some Googling, go and ask someone - we all have these problems. Things you can try first include trying a different compiler version, or an entirely different compiler e.g. pgi rather than ifort for example. You should bear in mind that as mentioned above, not all versions of each code will compile with every compiler. Make sure you're not trying to build something that isn't expected to work.

==Extra command line build examples==
The below commands are absolutely not an exhaustive list, but should give you an idea of what is possible. You can use ''ccmake'' as described above to discover which variables (e.g. WITH_AMBER) can be manipulated on the command line like this. All of these examples assume your svn repository is set up in ''/home/CRSID/svn'' - make the appropriate modifications if you have it elsewhere.

===GMIN===
'''A12GMIN''' (GMIN with AMBER12) using ifort:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/ifort_amber12
cd !$
FC=ifort cmake -DWITH_AMBER12=1 ../../source
make -j8
</pre>

'''C35GMIN''' (GMIN with CHARMM 35) using pgi:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/pgi_charmm35
cd !$
FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source
make -j8
</pre>

'''CUDAGMIN''' (GMIN leveraging GPU minimisation via the AMBER 12 interface) using ifort:
<pre>
module load cuda/5.5
mkdir -p ~/softwarewales/GMIN/builds/ifort_cuda
cd !$
FC=ifort cmake -DWITH_CUDA=1 ../../source
make -j8
</pre>
This will only work on machines with specific NVIDIA GPUs, for example when submitting jobs on the pat cluster. There is some additional information on the [[Using GMIN with GPUs]] page.

===OPTIM===
'''A9OPTIM''' (OPTIM with AMBER9) using ifort:
<pre>
mkdir -p ~/softwarewales/OPTIM/builds/ifort_amber
cd !$
FC=ifort cmake -DWITH_AMBER9=1 ../../source
make -j8
</pre>

'''C35OPTIM''' (OPTIM with CHARMM 35) using pgi:
<pre>
mkdir -p ~/softwarewales/OPTIM/builds/pgi_charmm35
cd !$
FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source
make -j8
</pre>

'''CUDAOPTIM''' (OPTIM leveraging GPU via the AMBER 12 interface) using ifort:
<pre>
module load cuda/5.5
mkdir -p ~/softwarewales/OPTIM/builds/ifort_cuda5.5
cd !$
FC=ifort CC=icc cmake -DWITH_CUDA=1 ../../source
make -j8
</pre>
This will only work on machines with specific NVIDIA GPUs, for example when submitting jobs on the pat cluster. There is some additional information on the [[Using GMIN and OPTIM with GPUs]] page.

===PATHSAMPLE===
There are very few options for [[PATHSAMPLE]] as we don't need to worry about interfacing with a particular potential. As a result, every binary is simply called ''PATHSAMPLE''.

Using nagfor (the NAG fortran compiler - check you have the module loaded - very strict!):
<pre>
mkdir -p ~/softwarewales/PATHSAMPLE/builds/nagfor
cd !$
FC=nagfor cmake ../../source
make -j8
</pre>

Using pgi (much more generous with coding slips/non-standard uses):
<pre>
mkdir -p ~/softwarewales/PATHSAMPLE/builds/pgi
cd !$
FC=pgf90 cmake ../../source
make -j8
</pre>

==Configuring defaults - for developers==

Fortran compilers and their corresponding default settings are all controlled by the file $SVN/CMakeModules/FindFORTRANCOMPILER.cmake ($SVN is your svn root directory). In particular, we may wish to edit the flags used for each set of compilers and build type. These are contained in the following block:

<pre>
if(NOT COMPILER_FLAGS_WERE_SET)
message("Setting initial values for compiler flags")
if(COMPILER_SWITCH MATCHES "pgi")
set (CMAKE_Fortran_FLAGS "-Mextend" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -Munroll -Mnoframe" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-Mextend -C -g -gopt -Mbounds -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -Mdwarf1 -Mdwarf2 -Melf -Mpgicoff -traceback" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-Mextend -C -g -gopt -Mbounds -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -Mdwarf1 -Mdwarf2 -Mdwarf3 -Melf -Mpgicoff -traceback" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-Mfree" CACHE TYPE STRING)
elseif(COMPILER_SWITCH MATCHES "gfortran")
set (CMAKE_Fortran_FLAGS "-ffixed-line-length-200 -ffree-line-length-0" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE TYPE STRING FORCE)
# set (CMAKE_Fortran_FLAGS_DEBUG "-g -fbounds-check -Wuninitialized -O -ftrapv -fimplicit-none -fno-automatic" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-g -fbounds-check -Wuninitialized -O -ftrapv -fno-automatic" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "${CMAKE_Fortran_FLAGS_DEBUG} -fimplicit-none" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-ffree-form" CACHE TYPE STRING)
elseif(COMPILER_SWITCH MATCHES "nag")
set (CMAKE_Fortran_FLAGS "-132 -kind=byte -maxcontin=3000" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-mismatch_all -O4" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-g -mismatch_all -ieee=stop" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-C=all -mtrace=all -gline -g -mismatch_all -ieee=stop" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-free" CACHE TYPE STRING) # js850> is this ever used?
elseif(COMPILER_SWITCH MATCHES "ifort")
set (CMAKE_Fortran_FLAGS "-132 -heap-arrays -assume byterecl" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE TYPE STRING FORCE)
# Warnings about temporary argument creation and edit descriptor widths are disabled with the final flags.
set (CMAKE_Fortran_FLAGS_DEBUG "-C -g -traceback -debug full -check all,noarg_temp_created -diag-disable 8290,8291" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-debug all -check all -implicitnone -warn unused -fp-stack-check -ftrapuv -check pointers -check bounds" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-free" CACHE TYPE STRING)
else()
message(FATAL_ERROR "unknown comiler switch: ${COMPILER_SWITCH}")
endif()
SET(COMPILER_FLAGS_WERE_SET yes CACHE TYPE INTERNAL)
endif(NOT COMPILER_FLAGS_WERE_SET)
</pre>

The main if/elseif blocks correspond to compiler switches. Inside these, there are the default flags for each of our build types (release, debug and debug_slow), which are configured using ccmake. These can be edited, if we wish to change the default behaviour (e.g. a recent addition of -check all,noarg_temp_created -diag-disable 8290,8291 to disable annoying warning messages for ifort).

Preparing an AMBER topology file for a protein system

2021-07-19T18:18:17Z

Nn320:

When you want to use [[AMBER]], either on its own to run MD, or interfaced with any of the group software ([[GMIN]], [[OPTIM]] or [[PATHSAMPLE]]), you need to have two files at your disposal. These are the topology file (which describes the atom types, connectivity of atoms, force field parameters for angles, etc.) and the coordinate file (which shockingly defines the coordinates of the atoms in your system).

To start work with [[AMBER]] you need files defining your system (topology and coordinates) and driving file with keyword defining conditions for molecular dynamics. The detailed tutorial referring specially to point 3 (how to get the topology and coordinate files for system with ligand) is presented in tutorial [[Preparing an AMBER topology file for a protein plus ligand system]].

It is important that one uses the symmetrised version of the parameters that Edyta work. These are available
via svn in AMBERTOOLS. When calling ''tleap'' it is important that you are using the version in AMBERTOOLS which
utilises the correct version of these parameters. If not one could have some unfortunate problems when making
connective with OPTIM and PATHSAMPLE. Below you can find simple LEaP scripts generating topology and coordinate files for three exemplary cases. In each case you need to run ONE of the following commands:

xleap -f leap.in
xleap < leap.in
tleap -f leap.in
tleap < leap.in

where ''leap.in'' is a name of the script.

''xleap'' is a graphical version of ''tleap'' therefore sometimes is easier to call ''tleap'' in the form of a script.

'''1. Generate topology and coordinate files. '''

You need to build a peptide from a sequence:

source leaprc.ff03
mol = sequence {NALA ALA ALA ALA ALA ALA ALA CALA}
saveamberparm mol mol.prmtop mol.inpcrd
savepdb mol mol.pdb
quit

or you can build a protein from an existing pdb file. There are two energy function that are most likely to
be used an ALL-ATOM model or an UNITED ATOM model. For the ALL-ATOM model ''source leaprc.ff03'' or an UNITED
ATOM model ''source leaprc.ff03ua''

source leaprc.ff03
mol=loadpdb protein.pdb.
saveamberparm mol mol.prmtop mol.inpcrd
savepdb mol mol.pdb
quit

On the beginning LEaP is reading force field parameters and AMBER libraries, and finally three files are produced: ''mol.prmtop'' with topology, ''mol.inpcrd'' with coordinates and ''mol.pdb'' which is PDB file that you can use to visualize the protein.

'''NOTE''': Remove all hydrogens belonging to amino acid and nucleic residues, LEaP will add them according to AMBER libraries. In case of wrong atom names or atoms types or residue names, you will find appropriate warnings in ''leap.log'' file which is output file from LEaP.

'''NOTE''': In case you want to use igb=8 implicit solvent model, add the following line to your leap.in file. (For more details, Ctrl+F igb=8 in AMBER manual)

set default PBradii mbondi3

'''2. Rename termini.'''

Now we have an AMBER topology file but there are a few changes we need to make before we can use it. The first is necessary and the second, while not essential - is highly recommended. The first step involves renaming the terminal residues.

When ''tleap'' created the topology file, it also renames the terminal residues, something we didn't want it to do! Open up [[Media:2hu4.top.txt | 2hu4.top]] in an editor and look for the section that begins with:
<pre>
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
</pre>
This is where the sequence is defined, however the N and C terminal residues should be named differently i.e. in our case VAL should be NVAL and ILE should be CILE. This edit isn't quite that simple however as the topology file uses a fixed format with four spaces per residue so you need to remove a blank space when you edit the name. e.g.

One can use a simpile sed command to swap the sequence out file the below commands. They need to be specified by
the unique sequence tag.
sed 's/^GLN GLN ASN ALA/NGLNGLN ASN ALA/' mol.prmtop > mol.prmtop.temp
sed 's/LEU ASN ASP ALA/LEU ASN ASP CALA/' mol.prmtop.temp > mol.prmtop

'''3. Symmeterize topology file.'''

If you followed the suggestions, you should have the scripts installed under svn already in the directory
/home/$USER/svn/SCRIPTS/AMBER/symmetrise_prmtop.

If you use the ALL-ATOM function you need to use a command like:

/home/$USER/svn/SCRIPTS/AMBER/symmetrise_prmtop/perm-prmtop.ff03.py mol.prmtop.old mol.prmtop

If you use the UNITED-ATOM function you need to use a command like:

/home/$USER/svn/SCRIPTS/AMBER/symmetrise_prmtop/perm-prmtop.ff03us.py mol.prmtop.old mol.prmtop

'''4. For OPTIM and PATHSAMPLE generate a perm.allow file.'''

If you followed the suggestions, you should have the scripts installed under svn already in the directory
/home/$USER/svn/SCRIPTS/make_perm.allow.

If you use the ALL-ATOM function you need to use a command like:

/home/$USER/svn/SCRIPTS/make_perm.allow/perm-pdb.py mol.prmtop.old mol.prmtop

If you use the UNITED-ATOM function you need to use a command like:

/home/$USER/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py mol.prmtop.old mol.prmtop

Compiling Wales Group codes using cmake

2021-01-11T17:00:50Z

Nn320: svn replaced with softwarewales

[http://www.cmake.org/ CMake] (Cross-platform Make) provides a simple, platform independent way for us to compile and test the group codebase. Dependencies are handled automatically, compilation can proceed in parallel to avoid long waits while testing changes and builds are done entirely outside of the source directory. It also enables us to use the [[Jenkins CI]] 'build bot' system to automatically compile and test the code on a nightly basis - helping us catch troublesome commits before they affect other users.

Although everything below refers to compiling [[GMIN]] with the Intel ''ifort'' compiler and AMBER9 - the exact same procedure works for [[OPTIM]] and [[PATHSAMPLE]].

Note that not every option for our codes is expected to actually compile with every compiler, for example, anything using CHARMM35/36 will not compile with ''nagfor'' or ''gfortran''. This is nothing to do with our code - it's a CHARMM issue. You can get an idea for what should work by looking at the automated [[Jenkins CI]] builds.

==Preparing to compile==
Before you get started, you need to ensure that the machine you are planning to compile on has cmake 2.8 or higher installed. You can check the current version like so:
<pre>
cmake --version
</pre>

The clusters have a module for cmake 3.0, which you can load using the following command:
<pre>
module load cmake/3.0.0
</pre>

You also need to create a directory to build the code in. We suggest that you create a directory for the compiler you are using within the program directory, under a subdirectory called 'builds' - for example for compiling GMIN with ifort, you would make a directory here:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/ifort
cd ~/softwarewales/GMIN/builds/ifort
</pre>
You can call these directories whatever you like - but make sure it is clear to you what they contain! You might also want to check which version of the compiler you have loaded. This is important as the different clusters and workstations may have different default versions loaded, some of which might not work properly. You can check the compiler version currently loaded using the same '--version' flag we used for ''cmake'' above:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ifort --version
ifort (IFORT) 12.1.3 20120212
Copyright (C) 1985-2012 Intel Corporation. All rights reserved.
</pre>

To load a different compiler, you can use the ''module load'' or ''module swap'' commands. A list of all available modules can be accessed using:
<pre>
module av
</pre>
If you are having problems compiling, one of the first things to check is whether it works with a different version of the compiler!

'''Note: When compiling GMIN, if you are getting the error that there is no implicit type for ERFC in ewald.f90, try using a newer version of your compiler. This should be the built-in complementary error function.'''

==Compiling using the ccmake GUI interface to set options==
[[Image:Ccmake.png|thumb|ccmake set up to compile A9GMIN|200px|right]]

One advantage using cmake has over make is that we can use the simple ccmake GUI. This interface lets us set options like compiling with AMBER9, or CHARMM35, toggle between 'Release' and 'Debug' builds (see below) - and examine and alter the flags being uses for the compilation if we wish. Before we can run ccmake, we need to specify the compiler and run cmake in our build directory (e.g. softwarewales/GMIN/builds/ifort). We specify the '''F'''ortran '''C'''ompiler by setting the '''$FC''' environment variable (in this case the Intel Fortran compiler, ifort), and then run ''cmake'' (on the command line), passing it the relative location of the [[GMIN]] source directory:
<pre>
FC=ifort cmake ../../source
</pre>

If you run ''ls'', you will see some cmake files have been generated:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ls
CMakeCache.txt CMakeFiles cmake_install.cmake Makefile modules
</pre>

You can now run ''ccmake'' to open the GUI:
<pre>
csw34@sinister:~/softwarewales/GMIN/builds/ifort> ccmake .
</pre>

To navigate between options, use the arrow keys. Options can be toggled by pressing Return. To compile [[GMIN]] with AMBER9 (A9GMIN), we need to toggle the ''WITH_AMBER'' option ''ON''. Once you have done this, you need to configure and generate appropriate cmake info. This is done by pressing 'c' to configure, 'e' to exit and then 'g' to generate.

'''Note: for some builds (CHARMM with DFTB and CUDAGMIN), you might need to configure, exit and generate twice to set all necessary options'''

You can now compile A9GMIN in parallel as follows:
<pre>
make -j8
</pre>

The '-j8' flag here tells make to use up to 8 'threads' when building. For optimal performance, you should keep this slightly greater than the number of cores (CPUs) the node you are working on has. If all goes well, you should now have an A9GMIN binary in your build directory - congratulations!
<pre>
Linking Fortran executable A9GMIN
[100%] Built target A9GMIN

--------------------------------------------------------------------------------------------- 15:23:45

csw34@sinister:~/softwarewales/GMIN/builds/ifort> ls
A9GMIN cmake_install.cmake libcudadummylib.a libmylapack.a NAB
AMBER display_version.f90 libdummylib.a Makefile nab_binaries_built
CMakeCache.txt GMIN libgminlib.a modules porfuncs.f90
CMakeFiles libamber12dummylib.a libmyblas.a n
</pre>
Plain [[GMIN]] is also built at the same time should you need it. You can move this into your ~/bin directory if you like, or anywhere else in your ''$PATH'' to make running it simple.

'''Note: If you want to use OPTIM with the new C++ implementation of the NEB routine, you will need to obtain the source code for that separately. See [https://wikis.ch.cam.ac.uk/wales/wiki/index.php/OPTIM here] for instructions.'''

==Compiling by setting options on the command line==
If you know the options you'd like to set already (you can see them all in ccmake), you can save some time by passing them directly to ''cmake'' on the command line, bypassing the need for ''ccmake''. For example, to compile A9GMIN (GMIN with the AMBER9 interface) using the Intel ifort compiler, you would run the following commands:
<pre>
FC=ifort cmake -DWITH_AMBER=1 ../../source
make -j8
</pre>
where '../../source' is the relative location of the GMIN source directory. You can find some more examples of compiling from the command line below.

==Compiling with MPI==
To compile with MPI support add the following flags when running cmake on the command line:
<pre>
FC=mpif90 CC=mpicc cmake ../source -DCOMPILER_SWITCH=pgi -DWITH_MPI=yes
</pre>
Here -DCOMPILER_SWITCH=pgi assumes you're using the Portland ''pgi'' compiler. Make sure you have the correct modules loaded (in this case ''pgi'' and ''mpi-pgi''), and that the particular mpi you want (in this case ''mpi-pgi'') is listed before any other mpi's loaded (so that it has the highest priority). The modules can be loaded by typing:
<pre>
module load pgi/64/
module load mpi/openmpi/pgi/64/1.6.3
</pre>

and you can check which modules are loaded and in which order/priority by the ''module list'' command. You may need to ''module unload <name>'' any other mpi's that are higher up in the list than the one you want. You can of course set the COMPILER_SWITCH and WITH_MPI flags in ''ccmake'' if you prefer.

Note: It has been observed that pgi/64/15.1 leads to compilation errors, and for now, it is best to use pgi/64/14.9

==Advanced mode - changing compiler flags with ccmake==
[[Image:Ccmakeadvanced.png|thumb|ccmake advanced mode|200px|right]]

Although initially the ''ccmake'' GUI looks very simple, there is a lot going on under the hood. By pressing 't' you can enter 'Advanced mode' which will show you all of the hidden options, for example the compiler flags that are being passed to ''make'' when you compile the code. You can also make changes to the flags here, for example if you would like to add '-p' to do profiling.

As with changing the build type, you simply select the field you'd like to change using the arrow keys, press Return, make your changes and press Return again to save them. When you subsequently configure and generate as above, those altered flag will be used for the subsequent compilation.

Note that these changes only apply in the build directory in which you make them.

==Debugging runtime problems using gdb or valgrind==
If you are getting a segmentation fault, crash or other unexpected behaviour, you might want to run your job through a debugger like [http://www.gnu.org/software/gdb/ gdb] or [http://valgrind.org/ valgrind]. In order to maximise your chances of getting useful output, you should build a 'Debug' version of the program you are having trouble. To do this, you can either change the ''CMAKE_BUILD_TYPE'' in ''ccmake'' to 'Debug' (press Return, change 'Release' to 'Debug' and press Return again), or on the command line like so for GMIN with AMBER 9 using the Intel ifort compiler:
<pre>
FC=ifort cmake -DCMAKE_BUILD_TYPE=Debug -DWITH_AMBER=1 ../../source
make -j8
</pre>

You can then run the binary ''through'' gdb or valgrind as follows:
<pre>
gdb A9GMIN
</pre>
or
<pre>
valgrind A9GMIN
</pre>

I won't cover debugging with these tools here as it's a science in itself! Do some Googling and ask for help as needed :)

==Debugging compilation problems==
There are many ways to try and track down why your code is not compiling. Before you start changing compilers, building a 'Debug' version or changing machines, you might want to try running make again with the ''VERBOSE'' option enabled. This will dump a lot of potentially useful output:
<pre>
VERBOSE=1 make
</pre>

One possible gotcha: all .f and .f90 files in the relevant source directories will be compiled and added to a library. This is quite different from the old Makefile way of doing things, where source files were explicitly specified for compilation (via their corresponding .o file). So, if you are testing something by for instance copying code.f90 to code.myhack.f90 and code.orig.f90, then slightly editing a line or two of code.myhack.f90 and copying it back to code.f90 for use, this will probably cause linking problems due to multiply-defined subroutines (from all three files). The solution, if you must have alternative versions of the same file hanging round, is to differentiate the filenames by a suffix AFTER the .f[90] .

Another occasional issue is the unexplained compiler bug - a problem with the version of the compiler you happen to be using. You can can an idea for which compiler versions we expect to work by checking the Jenkins build-bot output, as described in the 'Seeing console output' section of the [[Jenkins CI]] page. If you are using a different version of the compiler in question, consider swapping to the version Jenkins is using with 'module swap'.

If the error message you are getting doesn't make sense to you after some Googling, go and ask someone - we all have these problems. Things you can try first include trying a different compiler version, or an entirely different compiler e.g. pgi rather than ifort for example. You should bear in mind that as mentioned above, not all versions of each code will compile with every compiler. Make sure you're not trying to build something that isn't expected to work.

==Extra command line build examples==
The below commands are absolutely not an exhaustive list, but should give you an idea of what is possible. You can use ''ccmake'' as described above to discover which variables (e.g. WITH_AMBER) can be manipulated on the command line like this. All of these examples assume your svn repository is set up in ''/home/CRSID/svn'' - make the appropriate modifications if you have it elsewhere.

===GMIN===
'''A12GMIN''' (GMIN with AMBER12) using ifort:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/ifort_amber12
cd !$
FC=ifort cmake -DWITH_AMBER12=1 ../../source
make -j8
</pre>

'''C35GMIN''' (GMIN with CHARMM 35) using pgi:
<pre>
mkdir -p ~/softwarewales/GMIN/builds/pgi_charmm35
cd !$
FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source
make -j8
</pre>

'''CUDAGMIN''' (GMIN leveraging GPU minimisation via the AMBER 12 interface) using ifort:
<pre>
module load cuda/5.5
mkdir -p ~/softwarewales/GMIN/builds/ifort_cuda
cd !$
FC=ifort cmake -DWITH_CUDA=1 ../../source
make -j8
</pre>
This will only work on machines with specific NVIDIA GPUs, for example when submitting jobs on the pat cluster. There is some additional information on the [[Using GMIN with GPUs]] page.

===OPTIM===
'''A9OPTIM''' (OPTIM with AMBER9) using ifort:
<pre>
mkdir -p ~/softwarewales/OPTIM/builds/ifort_amber
cd !$
FC=ifort cmake -DWITH_AMBER9=1 ../../source
make -j8
</pre>

'''C35OPTIM''' (OPTIM with CHARMM 35) using pgi:
<pre>
mkdir -p ~/softwarewales/OPTIM/builds/pgi_charmm35
cd !$
FC=pgf90 cmake -DWITH_CHARMM35=1 ../../source
make -j8
</pre>

'''CUDAOPTIM''' (OPTIM leveraging GPU via the AMBER 12 interface) using ifort:
<pre>
module load cuda/5.5
mkdir -p ~/softwarewales/OPTIM/builds/ifort_cuda5.5
cd !$
FC=ifort CC=icc cmake -DWITH_CUDA=1 ../../source
make -j8
</pre>
This will only work on machines with specific NVIDIA GPUs, for example when submitting jobs on the pat cluster. There is some additional information on the [[Using GMIN and OPTIM with GPUs]] page.

===PATHSAMPLE===
There are very few options for [[PATHSAMPLE]] as we don't need to worry about interfacing with a particular potential. As a result, every binary is simply called ''PATHSAMPLE''.

Using nagfor (the NAG fortran compiler - check you have the module loaded - very strict!):
<pre>
mkdir -p ~/softwarewales/PATHSAMPLE/builds/nagfor
cd !$
FC=nagfor cmake ../../source
make -j8
</pre>

Using pgi (much more generous with coding slips/non-standard uses):
<pre>
mkdir -p ~/softwarewales/PATHSAMPLE/builds/pgi
cd !$
FC=pgf90 cmake ../../source
make -j8
</pre>

==Configuring defaults - for developers==

Fortran compilers and their corresponding default settings are all controlled by the file $SVN/CMakeModules/FindFORTRANCOMPILER.cmake ($SVN is your svn root directory). In particular, we may wish to edit the flags used for each set of compilers and build type. These are contained in the following block:

<pre>
if(NOT COMPILER_FLAGS_WERE_SET)
message("Setting initial values for compiler flags")
if(COMPILER_SWITCH MATCHES "pgi")
set (CMAKE_Fortran_FLAGS "-Mextend" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3 -Munroll -Mnoframe" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-Mextend -C -g -gopt -Mbounds -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -Mdwarf1 -Mdwarf2 -Melf -Mpgicoff -traceback" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-Mextend -C -g -gopt -Mbounds -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -Mdwarf1 -Mdwarf2 -Mdwarf3 -Melf -Mpgicoff -traceback" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-Mfree" CACHE TYPE STRING)
elseif(COMPILER_SWITCH MATCHES "gfortran")
set (CMAKE_Fortran_FLAGS "-ffixed-line-length-200 -ffree-line-length-0" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE TYPE STRING FORCE)
# set (CMAKE_Fortran_FLAGS_DEBUG "-g -fbounds-check -Wuninitialized -O -ftrapv -fimplicit-none -fno-automatic" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-g -fbounds-check -Wuninitialized -O -ftrapv -fno-automatic" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "${CMAKE_Fortran_FLAGS_DEBUG} -fimplicit-none" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-ffree-form" CACHE TYPE STRING)
elseif(COMPILER_SWITCH MATCHES "nag")
set (CMAKE_Fortran_FLAGS "-132 -kind=byte -maxcontin=3000" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-mismatch_all -O4" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG "-g -mismatch_all -ieee=stop" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-C=all -mtrace=all -gline -g -mismatch_all -ieee=stop" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-free" CACHE TYPE STRING) # js850> is this ever used?
elseif(COMPILER_SWITCH MATCHES "ifort")
set (CMAKE_Fortran_FLAGS "-132 -heap-arrays -assume byterecl" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_RELEASE "-O3" CACHE TYPE STRING FORCE)
# Warnings about temporary argument creation and edit descriptor widths are disabled with the final flags.
set (CMAKE_Fortran_FLAGS_DEBUG "-C -g -traceback -debug full -check all,noarg_temp_created -diag-disable 8290,8291" CACHE TYPE STRING FORCE)
set (CMAKE_Fortran_FLAGS_DEBUG_SLOW "-debug all -check all -implicitnone -warn unused -fp-stack-check -ftrapuv -check pointers -check bounds" CACHE TYPE STRING FORCE)
set (FORTRAN_FREEFORM_FLAG "-free" CACHE TYPE STRING)
else()
message(FATAL_ERROR "unknown comiler switch: ${COMPILER_SWITCH}")
endif()
SET(COMPILER_FLAGS_WERE_SET yes CACHE TYPE INTERNAL)
endif(NOT COMPILER_FLAGS_WERE_SET)
</pre>

The main if/elseif blocks correspond to compiler switches. Inside these, there are the default flags for each of our build types (release, debug and debug_slow), which are configured using ccmake. These can be edited, if we wish to change the default behaviour (e.g. a recent addition of -check all,noarg_temp_created -diag-disable 8290,8291 to disable annoying warning messages for ifort).

Managing interactive jobs on cluster

2020-05-18T11:20:03Z

Nn320: Created page with "When using cluster it is important to know how to manage interactive jobs. We may want to know what all jobs are running, what all jobs a particular user is running and how to..."

When using cluster it is important to know how to manage interactive jobs. We may want to know what all jobs are running, what all jobs a particular user is running and how to kill a particular job. The following bash commands are useful for this purpose: top, ps and kill.

===top===
top command is used to list the processes running on the system in real time. To exit from the top window press q . top command has several useful options.
* top -u CRSid is used to list the jobs of a particular user.
* top -n 1 -b > output can be used to save the top window to a file.
In top window itself
* pressing z highlights the running process.
* pressing c shows absolute path of all running processes.
* pressing k displays a line in top window where the process id (pid) of the process that needs to be killed can be directly entered and when asked about confirmation simply press y to kill the process.
* pressing Shift+o opens a new window with several options along with the corresponding letter that needs to be pressed to sort the top window based on a particular column. For example to sort all processes depending on memory usage i.e. %MEM press shift+o, n and Enter .
There is a lot more that can be done using top and more information can be found on its man page.

===ps===
ps stands for process status. One of its use can be to view the jobs of a particular user.
<pre> ps aux | egrep CRSid </pre>
 ps aux displays all processes along with usernames and egrep CRSid can be used to extract processes belonging to a particular user.
===kill===
kill can be used to kill a process. When running an interactive job, its execution can be stopped by pressing Ctrl+z and then kill command can be used.
<pre>
kill signal pid
</pre>
 kill -9 pid can be used to kill the process immediately. The option -9 stands for SIGKILL. More information about different types of signals can be found here https://en.wikipedia.org/wiki/Signal_(IPC)#List_of_signals

Comprehensive Contents Page

2020-05-18T11:12:55Z

Nn320: /* Cluster queues */

This page is designed to organise all of the pages on this wiki, as well as provide other useful links. Note that some pages may appear under more than one heading.

== Getting Started ==
[[Wales Group]] provides good step-by-step instructions. Relevant pages are:

=== Acquiring and compiling the group software ===
* [[SVN setup]]
* [[Wales Group Version control]] - to keep the code standardised.
* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.
* [[Compiling Wales Group codes using cmake]] - CMake (Cross-platform Make) allows us to compile and test the group codebase regardless of platform. This page provides crucial information how to compile using cmake.
* [[ElaborateDiff]]

=== Maintaining code health ===
* [[Jenkins CI]] - explains Jenkins, which we use to download our code and compile each of our targets with each of the compilers every night.
* https://wales-jenkins.ch.cam.ac.uk/ - log for our Jenkins tests.
* [[Branching and Merging]]
* [[Cmake interface building]]
* [[Installing python modules]]
* [[Revamping the modules system]]

=== Collaborators without access to the SVN repository ===
For licensing reasons, some code cannot be included in the Wales Group public tarball.
* http://www-wales.ch.cam.ac.uk/svn.tar.bz2 - Wales group public tarball. Includes [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]].
If a collaborator has a [[CHARMM]] or [[AMBER]] licence, we do maintain separate tarballs which include the [[CHARMM]], [[AMBER]] and [[CHARMM]]+[[AMBER]] source and interfaces. These are not linked anywhere on the website and require a username ('''wales''') and password ('''group''') to download:

* [http://www-wales.ch.cam.ac.uk/CHARMM/svn.CHARMM.tar.bz2 CHARMM]
* [http://www-wales.ch.cam.ac.uk/AMBER/svn.AMBER.tar.bz2 AMBER]
* [http://www-wales.ch.cam.ac.uk/both/svn.both.tar.bz2 AMBER+CHARMM]

=== Running on Windows ===
Not particularly recommended.
* [[Running Wales Group software on Windows 7]]

== Wales Group Programs ==

=== Programs ===
* [[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
* [[OPTIM]]: A program for optimizing geometries and calculating reaction pathways.
* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.

=== Curated Examples ===
* https://github.com/wales-group/examples - set of tutorials detailing how to use GMIN, OPTIM and PATHSAMPLE. Essential for beginners.
* http://www-wales.ch.cam.ac.uk/VM/Wales_Group_VM.ova - Pre-prepared teaching virtual machine. This contains the code and examples.
* https://www.virtualbox.org/wiki/Downloads - This is required if using the VM above.
* https://github.com/wales-group/examples.git - Alternatively, you can run the examples on your own machine. To get hold of the relevant files:
<pre>
git clone https://github.com/wales-group/examples.git
</pre>

== Useful Notes on Wales Group Programs and Subroutines ==
=== [[GMIN]] ===
* [[Adding a model to GMIN]] - rough outline of the subroutines that need to be changed to add a new model to GMIN
* [[Compiling Wales Group codes using cmake | Compiling GMIN using cmake ]]
* [[Selecting search parameters for GMIN]]
* [[Global optimization of biomolecules using CHARMM]]
* [[Global optimization of biomolecules using AMBER9]]
* [[Global optimization of biomolecules using AMBER9 with Structural Restraints]]
* [[Calculating binding free energy using the FSA method]]
* [[Restarting a GMIN run from a dump file]]
* [[Using the implicit membrane model IMM1]]
* [[Running a Go model with the AMHGMIN]]
* [[Running a G\=o model with the AMHGMIN]]
* [[Ligand binding-mode searches with HBONDMATRIX]]
* [[Compiling and using GMIN with QUIP]]
* [[Using GMIN and OPTIM with GPUs]]
* [[Using GMIN to generate endpoints]]
* [[Using GMIN to generate endpoints (CHARMM)]]
* [[Generating a GMIN Eclipse project]]
* [[Mutational BH steps]]
* [[Biomolecules in the energy landscape framework]]
* [[DMAGMIN setup]]
* [[Keywords]]
* [[PYGMIN & DMACRYS]]
* [[Rotamer moves in AMBER]]
* [[Python interface for GMIN/OPTIM]]

==== Scripts ====
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining

==== Useful info for coding GMIN ====
* [[Program flow]] - contains information about what the various files in GMIN do and what order they're called.
* [[amberinterface]]

==== Projects ====
* [[GMIN MOVES module]]
* [[GMIN SANITY module]]
* [[GMIN TESTS module]]
* [[CAMSHIFT]]

=== [[OPTIM]] ===
* [[Adding a model to OPTIM]] - rough outline of the subrounties that need to be changed to add a new model to OPTIM
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[visualising normal modes using VMD and OPTIM]]
* [[Compiling Wales Group codes using cmake | Compiling OPTIM using cmake ]]
* [[OPTIM/Q-Chem Tutorial]]
* [[OPTIM and PY ellipsoids tutorial]]
* [[OPTIM output files]]
* [[Minimizing a structure using OPTIM and AMBER9]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Creating movies (.mpg) of paths using OPTIM]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Debugging odd transition states in OPTIM]]
* [[Connecting two minima with a pathway]] - step by step
* [[Compiling and using OPTIM with QUIP]]
* [[Running an Gaussian03 interfaced OPTIM job]]
* [[The effect of calculating less than the maximum number of eigenvalues using ENDHESS n]]
* [[Biomolecules in the energy landscape framework]]
* [[BLJ60 example setup]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Python interface for GMIN/OPTIM]]
* [[Thomson problem in OPTIM]]
* [[Instanton tunneling and classical rate calculations with OPTIM]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[common setup problem : No Frequency Warning]]

=== [[PATHSAMPLE]] ===
* [[Adding a model to PATHSAMPLE]] - rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[Compiling Wales Group codes using cmake | Compiling PATHSAMPLE using cmake ]]
* [[IMPORTANT: Using PATHSAMPLE safely on sinister]]
* [[Adding a model for PATHSAMPLE]]
* [[List of output files for PATHSAMPLE]]
* [[Using BHINTERP to find minima between two end points]]
* [[Finding an initial path between two end points (minima)]]
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[Optimising a path]]
* [[Fine tuning UNTRAP]] - ensuring that it picks sensible minima
* [[Calculating rate constants (GT and fastest path)]]
* [[Calculating rate constants (SGT, DGT, and SDGT)]]
* [[Identifying the k fastest paths between endpoints using KSHORTESTPATHS]]
* [[Removing minima and transition states from the database]]
* [[Relaxing existing minima with new potential and creating new database]]
* [[Relaxing existing transition states with new potential and creating new database]]
* [[If things go wrong...]]
* [[If you lost file min.data, but still you have points.min]]
* [[path.info file is not read, causes PATHSAMPLE to die]]
* [[BLJ60 example setup]]
* [[When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path]]
* [[Biomolecules in PATHSAMPLE]]
* [[Biomolecules in the energy landscape framework]]
* [[Expanding the kinetic transition network with PATHSAMPLE]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths]]
* [[Pathsampling short paths (CHARMM)]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[Connecting Sub-databases]]

=== [[Notes on MINPERMDIST | MINPERMDIST]] ===

=== [[Quasi-continuous interpolation for biomolecules | QCI]] ===

== Non-Group Software ==

=== [[AMBER]] ===
Molecular dynamics simulation program and associated force fields.
* [http://ambermd.org/ AMBER]
* [http://ambermd.org/tutorials/ AMBER tutorials] - recommended reading for '''ANYONE''' using AMBER!
* [[Notes on AMBER 12 interface]]
* [[Using AMBER 14 on the GPU and compute clusters]]
* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
* [[Generating parameters using RESP charges from GAMESS-US]]
* [[Simple scripts for LEaP to create topology and coordinate files]]
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[Using Molfacture to edit molecules and add hydrogens]]
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide
* [[Symmetrising AMBER topology files]] - step by step guide for symmetrising a complex protein+ligand system
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb''
* [[Running GMIN with MD move steps AMBER]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Evaluating different components of AMBER energy function with SANDER]]
* [[Mutational BH steps]]
* [[REMD with AMBER]]
* [[Performing a hydrogen-bond analysis]]
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Biomolecules in the energy landscape framework]]
* [[perm-prmtop.py]] - A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[Rotamer moves in AMBER]]
* [[Creating mismatched DNA duplex using NAB]]

=== [[aux2bib]] ===
To generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.
* [https://ctan.org/pkg/bibtools Get script here]

=== [[CamCasp]] ===
Cambridge package for Calculation of Anisotropic Site Properties
From Anthony Stone's website: 'CamCASP is a collection of scripts and programs written by Dr Alston Misquitta and myself for the calculation ab initio of distributed multipoles, polarizabilities, dispersion coefficients and repulsion parameters for individual molecules, and interaction energies between pairs of molecules using SAPT(DFT).'
* [http://www-stone.ch.cam.ac.uk/programs.html CamCASP home]
* [[CamCASP/Programming]]
* [[CamCASP/Programming/5/example1]]
* [[CamCASP/Notes]]
* [[CamCASP/Bugs]]
* [[CamCASP/ToDo/diskIO]]
* [[CamCASP/ToDo/Memory]]
* [[CamCASP/CodeExamples/DirectAccess]]

=== [[CPMD]] ===
Implementation of DFT for ''ab-initio'' molecular dynamics.
* [http://www.cpmd.org/ Home Page]
* [[CPMDInput]]

=== [[CHARMM]] ===
Molecular dynamics simulation program and associated force fields.
* [https://www.charmm.org/charmm/?CFID=65f7b3aa-8037-452a-bcd1-7583dd83a087&CFTOKEN=0 CHARMM]
* [[Generating pdb, crd and psf for a peptide sequence]]
* [[Converting between '.crd' and '.pdb']]
* [[Calculating energy of a conformation]]
* [[Calculating molecular properties]]
* [[Calculating order parameters]]
* [[CAMSHIFT]]
* [[Setting up (CHARMM)]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths (CHARMM)]]

=== [[disconnectionDPS]] ===
Produces disconnectivity graphs from min.data and ts.data files. This is included in the Wales group public tarball.
* [[Constructing Free Energy Disconnectivity Graphs]]

=== [[DMACRYS]] ===
Package which models crystals of rigid molecules.
* [http://www.chem.ucl.ac.uk/cposs/dmacrys/index.html Home Page]
* [[DMACRYS interface]]
* [[DMAGMIN setup]]
* [[PYGMIN & DMACRYS]]

=== [[GAMESS]] ===
General ''ab initio'' quantum chemistry package.
* [https://www.msg.chem.iastate.edu/gamess/ GAMESS]

=== [[Gaussian]] ===
General purpose package for computational chemistry calculations.
* [[Running an Gaussian03 interfaced OPTIM job]]

=== [[gnuplot]] ===
Open source graphing program.
* [http://www.gnuplot.info/ gnuplot]
* [[Plotting a quick histogram in gnuplot using the raw data]]
* [[Plotting data in real time]]
* [[Linear and non-linear regression in gnuplot]]

=== [[GROMACS]] ===
Molecular dynamics package.
* [[Installing GROMACS on Clust]]
* [http://www.mdtutorials.com/gmx/ External tutorials]
* [http://www.gromacs.org/Documentation/Tutorials More external tutorials]

=== [[HiRE-RNA]] ===
High-res course-grained energy model for RNA.
* [https://pubs.acs.org/doi/10.1021/jp102497y Explanatory Paper]

=== [[latex2html]] ===
Script which converts latex documents into HTML pages.
* [https://www.latex2html.org/ Get script here]

=== [[MMTSB-toolset]] ===
Group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD with CHARMM or AMBER.
* [http://feig.bch.msu.edu/mmtsb/Main_Page Documentation]
* [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html External tutorials]
* [[Installing and setting up the MMTSB toolset]]
* [[REX (Replica EXchange MD) with the MMTSB-toolset]]

=== [[Simulations using OPEP | OPEP]] ===
OPEP is a coarse-grained force field providing a potential for proteins and RNA.
* [http://opep.galaxy.ibpc.fr/ OPEP file generator here]
* [[Biomolecules in the energy landscape framework]]

=== [[pgprof]] ===
Profiler for portland-compiled codes
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

=== [[Pymol]] ===
Molecular visualisation program.
* [https://pymol.org/2/ PyMOL]
* [https://pymolwiki.org/index.php/Main_Page PyMOL Community Wiki]
* [[loading AMBER prmtop and inpcrd files into Pymol]]
* [[producing sexy ray-traced images]]
* [[advanced colouring]]
* [[Installing python modules]]
* [[PYGMIN & DMACRYS]]
* [[path2pdb.py]] - A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
=== [[VASP]] ===
OPTIM has an interface to VASP, which is installed on CSD3. In collaboration with Bora Karasulu the interface has been updated to use VASP format POSCAR input files for both single- and double-ended optimisations and path searches. The OPTIM odata file requires a line like

VASP 'mpirun -ppn 16 -np 16 /home/bk393/APPS/vasp.5.4.4/with-VTST/bin/vasp_std > vasp.out'

POSCAR files can be visualised using ase, the Atomic Simulation Environment, which can be accessed on volkhan via

module load anaconda/python3/5.3.0

pip install ase --user

ase-gui POSCAR1.vasp &

which assumes that ~/.input/bin is in your $PATH environment variable.

=== [[VMD]] ===
Molecular visualisation program.
* [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html Documentation]
* [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html External tutorials]
* [[using VMD to display and manipulate '.pdb' files]]
* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9
* [[visualising normal modes using VMD and OPTIM]]
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[Useful .vmdrc file]]
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
* [[VMD script to annotate each frame of a trajectory]]

=== [[xfig]] ===
Open source vector graphics editor
* [https://ctan.org/tex-archive/support/epstopdf/ Convert eps to pdf]

=== [[Xmakemol]] ===
Program for visualising atomic and molecular systems.
* [https://www.nongnu.org/xmakemol/ XMakemol]

=== [[xmgrace]] ===
2D plotting tool.
* [http://exciting-code.org/xmgrace-quickstart Xmgrace]

== Theoretical/Mathematical Notes ==

* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[Ellipsoid.model]]
* [[Ellipsoid.model.xyz]]
* [[Ellipsoid.xyz]]
* [[Gencoords]]
* [[GenCoords]]
* [[GenCoords Models]]
* [[Rotamer moves in AMBER]]
* [[Thomson problem in OPTIM]]

=== Angle-axis notes ===

* [[Angle-axis framework]]
* [[Computing normal modes in angle-axis]]

=== Rigid Bodies ===

* [[Automatic Rigid Body Grouping]]
* [[Rigid body input files for proteins using genrigid-input.py]]
* [[Local Rigid Body Framework]]
* [[Local rigid body in OPTIM]]

== Useful Scripts ==
* [[perm-prmtop.py]]: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[colourdiscon.py]]: A python program for sorting input for disconnectivity graphs
* [[pdb_to_movie.py]]: A python program to create an AMH movieseg file from a PDB file
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining
* [[recommended bash aliases]]
* [[David's .inputrc file]]
* [[Useful .vmdrc file]]
* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[GenCoords]]: A fortran program to generate coarse grain building blocks and initial coords using a set of geometric models.
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
See also the SCRIPTS/ directory in the SVN repository!
* [[Computing CHARMM FF energy using GMIN, MMTSB and CHARMM]] - Computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB options.
* [[Automatic Rigid Body Grouping]]
* [[ElaborateDiff]]
* [[Parameter-scanning script]]
* [[Pdb to movie.py]]
* [[VMD script to annotate each frame of a trajectory]]

== Useful links ==
* [http://www.ch.cam.ac.uk/computing/theory-compute-clusters The Theory Compute Clusters support page]. Contains useful cluster specific information, including example job submission scripts.

* A useful website which contains AMBER (GAFF) and OPLS parameters for small molecules. http://virtualchemistry.org/gmld.php . This could save us lot of time while trying to derive parameters on our own. If you are lucky, the molecule of your interest may already be there in the existing database. The topology files are in GROMACS format but possibly can be converted into AMBER parameter files. (script anyone ?)

* The moving-domain QM/MM method developed by Victor Batista's group http://gascon.chem.uconn.edu/software. This approach can be used in the derivation of charges for large proteins and nucleic acids, where a full-fledged ONIOM based calculation is comptutationally prohibitive. It has been applied to systems like the Gramicidin ion channel and Photosystem II.

== Miscellaneous ==
* [[Animated GIF on the group website]]
* [[Backup strategy]]
* [[Chain crossing]]
* [[Computer Office services]]
* [[Computing values only once]]
* [[Decoding heat capacity curves]]
* [[Differences from Clust]]
* [[Fixing thunderbird links]]
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Intel Trace Analyzer and Collector]]
* [[LDAP plans]]
* [[Lapack compilation]]
* [[Mek-quake Queueing system]]
* [[Mek-quake initial setup notes]]
* [[New mek-quake]]
* [[Maui compilation]]
* [[Torque and Maui]]
* [[Mercurial]]
* [[Migrating to the new SVN server]]
* [[NECI Parallelization]]
* [[Optimization tricks]]
* [[Other IT stuff]]
* [[Porfuncs Documentation]]
* [[Progress]]
* [[Proposed changes to backup and archiving]]
* [[Rama upgrade]]
* [[Remastering Knoppix]]
* [[See unpacked nodes]]
* [[Tardis scheduling policy]]
* [[Zippo Sicortex machine]]
* [[Beginner's guide to working in Wales group]]

== Useful linux stuff ==

===Basics===
* [[basic linux commands everyone should know!]]
* [[piping and redirecting output from one command or file to another]] - how to save yourself hours!
* [[bash loop tricks]]
* [[bash history searching]]

===Remote access===
* [[setting up aliases to quickly log you in to a different machine]]
* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''
* [[using 'ssh-keygen' to automatically log you into clusters from your workstation]] (no more typing in your password!)
* [[mounting sharedscratch locally]]

===Find and replace===
* [[short 'sed' examples]]
* [[quick guide to awk]]
* [[short 'awk' examples]]

===File manipulation===
* [[sorting a file by multiple columns]]
* [[using tar and gzip to compress/uncompress files | using tar and bzip2 to compress/uncompress files]]
* [[conversion between different data file formats]] -'almost one-line' scripts
* [[conversion between different image file formats]] - the ''convert'' command
* [[removing an excessive number of files from a directory - when 'rm' just isn't enough]]

===Cluster queues===
* [[submitting jobs, interactively or to a cluster queue system]]
* [[identifying job on a node]] - if you need to kill only one of few running jobs
* [[a guide to using SLURM to run PATHSAMPLE]]
* [[a guide to using SLURM to run GPU jobs on pat]]
* [[managing interactive jobs on cluster]]

===Miscellaneous/uncategorised===
* [[installing packages on your managed CUC3 workstation]]
* [[running programs in the background]] - so you can use your shell for other things at the same time
* [[finding bugs in latex documents that will not compile]]
* [[printing files from the command line using 'lpr']]
* [[uploading non image files to the wiki]]

== Compiler Flags ==

* [[Compiler Flags]]
* [[Blacklisting Compilers]]
* [[Lapack compilation]]
* [[Pdb to movie.py]]
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

== SuSE ==

* [[Upgrading destiny]]
* [[Upgrading sword]]
* [[SuSE 10.1 workstation image]]
* [[SuSE 10.2 workstation image]]
* [[SuSE 10.3 workstation image]]
* [[SuSE 11.1]]

--[[User:adk44|adk44]] 17.00, 9 May 2019 (BST)

Interactive jobs on cluster

2020-05-18T11:09:53Z

Nn320:

Interactive jobs on cluster

2020-05-18T11:08:13Z

Nn320:

When using cluster it is important to know how to manage interactive jobs. We may want to know what all jobs are running, what all jobs a particular user is running and how to kill a particular job. The following bash commands are useful for this purpose: top, ps and kill.

===top===
top command is used to list the processes running on the system in real time. To exit from the top window press q . top command has several useful options.
* top -u CRSid is used to list the jobs of a particular user
* top -n 1 -b > output can be used to save the top window to a file
In top window itself
* pressing z highlights the running process
* pressing c shows absolute path of all running processes
* pressing k displays a line in top window where the process id (pid) of the process that needs to be killed can be directly entered and when asked about confirmation simply press y to kill the process.
* pressing Shift+o opens a new window with several options along with the corresponding letter that needs to be pressed to sort the top window based on a particular column. For example to sort all processes depending on memory usage i.e. %MEM press shift+o, n and Enter .
There is a lot more that can be done using top and more information can be found on its man page.

===ps===
ps stands for process status. One of its use can be to view the jobs of a particular user.
<pre> ps aux | egrep CRSid </pre>
 ps aux displays all processes along with usernames and egrep CRSid can be used to extract processes belonging to a particular user.
===kill===
kill can be used to kill a process. When running an interactive job, its execution can be stopped by pressing Ctrl+z and then kill command can be used.
<pre>
kill signal pid
</pre>
 kill -9 pid can be used to kill the process immediately. The option -9 stands for SIGKILL. More information about different types of signals can be found here https://en.wikipedia.org/wiki/Signal_(IPC)#List_of_signals

Interactive jobs on cluster

2020-05-18T11:05:30Z

Nn320:

When using cluster it is important to know how to manage interactive jobs. We may want to know what all jobs are running, what all jobs a particular user is running and how to kill a particular job. The following bash commands are useful for the purpose: top, ps and kill.

===top===
top command is used to list the processes running on the system in real time. To exit from the top window press q . top command has several useful options.
* top -u CRSid is used to list the jobs of a particular user
* top -n 1 -b > output can be used to save the top window to a file
In top window itself
* pressing z highlights the running process
* pressing c shows absolute path of all running processes
* pressing k displays a line in top window where the process id (pid) of the process that needs to be killed can be directly entered and when asked about confirmation simply press y to kill the process.
* pressing Shift+o opens a new window with several options along with the corresponding letter that needs to be pressed to sort the top window based on a particular column. For example to sort all processes depending on memory usage i.e. %MEM press shift+o, n and Enter .
There is a lot more that can be done using top and more information can be found on its man page.

===ps===
ps stands for process status. One of its use can be to view the jobs of a particular user.
<pre> ps aux | egrep CRSid </pre>
The a, u and x in aux stand for displaying all processes along with usernames from which processes of a particular user can be extracted using egrep.

===kill===
kill can be used to kill a process. When running an interactive job, its execution can be stopped by pressing Ctrl+z and then kill command can be used.
<pre>
kill signal pid
</pre>
 kill -9 pid can be used to kill the process immediately. The option -9 stands for SIGKILL. More information about different types of signals can be found here https://en.wikipedia.org/wiki/Signal_(IPC)#List_of_signals

Interactive jobs on cluster

2020-05-18T10:55:31Z

When using cluster it is important to know how to manage interactive jobs. We may want to know what all jobs are running, what all jobs a particular user is running and how to kill a particular job. The following bash commands are useful for the purpose: top, ps and kill.

===top===
top command is used to list the processes running on the system in real time. To exit from the top window press q . top command has several useful options
* top -u CRSid is used to list the jobs of a particular user
* top -n 1 -b > output can be used to save the top window to a file
In top window itself
* pressing z highlights the running process
* pressing c shows absolute path of all running processes
* pressing k displays a line in top window where the process id (pid) of the process that needs to be killed can be directly entered and when asked about confirmation simply press y
* pressing Shift+o opens a new window with several options along with the corresponding letter that needs to be pressed to sort the top window based on a particular column.
There is a lot more that can be done using top and more information can be found on its man page.

===ps===
ps stands for process status. One of its use can be to view the jobs of a particular user.
<pre> ps aux | egrep CRSid </pre>
The a, u and x in aux stand for displaying all processes along with usernames and x stands for displaying even those processes not necessarily

===kill===
kill can be used to kill a process. When running an interactive job, its execution can be stopped by pressing Ctrl+z and then kill command can be used.
<pre>
kill signal pid
</pre>
kill -9 pid can be used to kill the process immediately. The option -9 stands for SIGKILL. More information about different types of signals can be found here https://en.wikipedia.org/wiki/Signal_(IPC)#List_of_signals

Comprehensive Contents Page

2020-05-18T10:15:33Z

Nn320: /* Cluster queues */

This page is designed to organise all of the pages on this wiki, as well as provide other useful links. Note that some pages may appear under more than one heading.

== Getting Started ==
[[Wales Group]] provides good step-by-step instructions. Relevant pages are:

=== Acquiring and compiling the group software ===
* [[SVN setup]]
* [[Wales Group Version control]] - to keep the code standardised.
* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.
* [[Compiling Wales Group codes using cmake]] - CMake (Cross-platform Make) allows us to compile and test the group codebase regardless of platform. This page provides crucial information how to compile using cmake.
* [[ElaborateDiff]]

=== Maintaining code health ===
* [[Jenkins CI]] - explains Jenkins, which we use to download our code and compile each of our targets with each of the compilers every night.
* https://wales-jenkins.ch.cam.ac.uk/ - log for our Jenkins tests.
* [[Branching and Merging]]
* [[Cmake interface building]]
* [[Installing python modules]]
* [[Revamping the modules system]]

=== Collaborators without access to the SVN repository ===
For licensing reasons, some code cannot be included in the Wales Group public tarball.
* http://www-wales.ch.cam.ac.uk/svn.tar.bz2 - Wales group public tarball. Includes [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]].
If a collaborator has a [[CHARMM]] or [[AMBER]] licence, we do maintain separate tarballs which include the [[CHARMM]], [[AMBER]] and [[CHARMM]]+[[AMBER]] source and interfaces. These are not linked anywhere on the website and require a username ('''wales''') and password ('''group''') to download:

* [http://www-wales.ch.cam.ac.uk/CHARMM/svn.CHARMM.tar.bz2 CHARMM]
* [http://www-wales.ch.cam.ac.uk/AMBER/svn.AMBER.tar.bz2 AMBER]
* [http://www-wales.ch.cam.ac.uk/both/svn.both.tar.bz2 AMBER+CHARMM]

=== Running on Windows ===
Not particularly recommended.
* [[Running Wales Group software on Windows 7]]

== Wales Group Programs ==

=== Programs ===
* [[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
* [[OPTIM]]: A program for optimizing geometries and calculating reaction pathways.
* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.

=== Curated Examples ===
* https://github.com/wales-group/examples - set of tutorials detailing how to use GMIN, OPTIM and PATHSAMPLE. Essential for beginners.
* http://www-wales.ch.cam.ac.uk/VM/Wales_Group_VM.ova - Pre-prepared teaching virtual machine. This contains the code and examples.
* https://www.virtualbox.org/wiki/Downloads - This is required if using the VM above.
* https://github.com/wales-group/examples.git - Alternatively, you can run the examples on your own machine. To get hold of the relevant files:
<pre>
git clone https://github.com/wales-group/examples.git
</pre>

== Useful Notes on Wales Group Programs and Subroutines ==
=== [[GMIN]] ===
* [[Adding a model to GMIN]] - rough outline of the subroutines that need to be changed to add a new model to GMIN
* [[Compiling Wales Group codes using cmake | Compiling GMIN using cmake ]]
* [[Selecting search parameters for GMIN]]
* [[Global optimization of biomolecules using CHARMM]]
* [[Global optimization of biomolecules using AMBER9]]
* [[Global optimization of biomolecules using AMBER9 with Structural Restraints]]
* [[Calculating binding free energy using the FSA method]]
* [[Restarting a GMIN run from a dump file]]
* [[Using the implicit membrane model IMM1]]
* [[Running a Go model with the AMHGMIN]]
* [[Running a G\=o model with the AMHGMIN]]
* [[Ligand binding-mode searches with HBONDMATRIX]]
* [[Compiling and using GMIN with QUIP]]
* [[Using GMIN and OPTIM with GPUs]]
* [[Using GMIN to generate endpoints]]
* [[Using GMIN to generate endpoints (CHARMM)]]
* [[Generating a GMIN Eclipse project]]
* [[Mutational BH steps]]
* [[Biomolecules in the energy landscape framework]]
* [[DMAGMIN setup]]
* [[Keywords]]
* [[PYGMIN & DMACRYS]]
* [[Rotamer moves in AMBER]]
* [[Python interface for GMIN/OPTIM]]

==== Scripts ====
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining

==== Useful info for coding GMIN ====
* [[Program flow]] - contains information about what the various files in GMIN do and what order they're called.
* [[amberinterface]]

==== Projects ====
* [[GMIN MOVES module]]
* [[GMIN SANITY module]]
* [[GMIN TESTS module]]
* [[CAMSHIFT]]

=== [[OPTIM]] ===
* [[Adding a model to OPTIM]] - rough outline of the subrounties that need to be changed to add a new model to OPTIM
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[visualising normal modes using VMD and OPTIM]]
* [[Compiling Wales Group codes using cmake | Compiling OPTIM using cmake ]]
* [[OPTIM/Q-Chem Tutorial]]
* [[OPTIM and PY ellipsoids tutorial]]
* [[OPTIM output files]]
* [[Minimizing a structure using OPTIM and AMBER9]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Creating movies (.mpg) of paths using OPTIM]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Debugging odd transition states in OPTIM]]
* [[Connecting two minima with a pathway]] - step by step
* [[Compiling and using OPTIM with QUIP]]
* [[Running an Gaussian03 interfaced OPTIM job]]
* [[The effect of calculating less than the maximum number of eigenvalues using ENDHESS n]]
* [[Biomolecules in the energy landscape framework]]
* [[BLJ60 example setup]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Python interface for GMIN/OPTIM]]
* [[Thomson problem in OPTIM]]
* [[Instanton tunneling and classical rate calculations with OPTIM]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[common setup problem : No Frequency Warning]]

=== [[PATHSAMPLE]] ===
* [[Adding a model to PATHSAMPLE]] - rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[Compiling Wales Group codes using cmake | Compiling PATHSAMPLE using cmake ]]
* [[IMPORTANT: Using PATHSAMPLE safely on sinister]]
* [[Adding a model for PATHSAMPLE]]
* [[List of output files for PATHSAMPLE]]
* [[Using BHINTERP to find minima between two end points]]
* [[Finding an initial path between two end points (minima)]]
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[Optimising a path]]
* [[Fine tuning UNTRAP]] - ensuring that it picks sensible minima
* [[Calculating rate constants (GT and fastest path)]]
* [[Calculating rate constants (SGT, DGT, and SDGT)]]
* [[Identifying the k fastest paths between endpoints using KSHORTESTPATHS]]
* [[Removing minima and transition states from the database]]
* [[Relaxing existing minima with new potential and creating new database]]
* [[Relaxing existing transition states with new potential and creating new database]]
* [[If things go wrong...]]
* [[If you lost file min.data, but still you have points.min]]
* [[path.info file is not read, causes PATHSAMPLE to die]]
* [[BLJ60 example setup]]
* [[When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path]]
* [[Biomolecules in PATHSAMPLE]]
* [[Biomolecules in the energy landscape framework]]
* [[Expanding the kinetic transition network with PATHSAMPLE]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths]]
* [[Pathsampling short paths (CHARMM)]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[Connecting Sub-databases]]

=== [[Notes on MINPERMDIST | MINPERMDIST]] ===

=== [[Quasi-continuous interpolation for biomolecules | QCI]] ===

== Non-Group Software ==

=== [[AMBER]] ===
Molecular dynamics simulation program and associated force fields.
* [http://ambermd.org/ AMBER]
* [http://ambermd.org/tutorials/ AMBER tutorials] - recommended reading for '''ANYONE''' using AMBER!
* [[Notes on AMBER 12 interface]]
* [[Using AMBER 14 on the GPU and compute clusters]]
* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
* [[Generating parameters using RESP charges from GAMESS-US]]
* [[Simple scripts for LEaP to create topology and coordinate files]]
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[Using Molfacture to edit molecules and add hydrogens]]
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide
* [[Symmetrising AMBER topology files]] - step by step guide for symmetrising a complex protein+ligand system
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb''
* [[Running GMIN with MD move steps AMBER]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Evaluating different components of AMBER energy function with SANDER]]
* [[Mutational BH steps]]
* [[REMD with AMBER]]
* [[Performing a hydrogen-bond analysis]]
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Biomolecules in the energy landscape framework]]
* [[perm-prmtop.py]] - A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[Rotamer moves in AMBER]]
* [[Creating mismatched DNA duplex using NAB]]

=== [[aux2bib]] ===
To generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.
* [https://ctan.org/pkg/bibtools Get script here]

=== [[CamCasp]] ===
Cambridge package for Calculation of Anisotropic Site Properties
From Anthony Stone's website: 'CamCASP is a collection of scripts and programs written by Dr Alston Misquitta and myself for the calculation ab initio of distributed multipoles, polarizabilities, dispersion coefficients and repulsion parameters for individual molecules, and interaction energies between pairs of molecules using SAPT(DFT).'
* [http://www-stone.ch.cam.ac.uk/programs.html CamCASP home]
* [[CamCASP/Programming]]
* [[CamCASP/Programming/5/example1]]
* [[CamCASP/Notes]]
* [[CamCASP/Bugs]]
* [[CamCASP/ToDo/diskIO]]
* [[CamCASP/ToDo/Memory]]
* [[CamCASP/CodeExamples/DirectAccess]]

=== [[CPMD]] ===
Implementation of DFT for ''ab-initio'' molecular dynamics.
* [http://www.cpmd.org/ Home Page]
* [[CPMDInput]]

=== [[CHARMM]] ===
Molecular dynamics simulation program and associated force fields.
* [https://www.charmm.org/charmm/?CFID=65f7b3aa-8037-452a-bcd1-7583dd83a087&CFTOKEN=0 CHARMM]
* [[Generating pdb, crd and psf for a peptide sequence]]
* [[Converting between '.crd' and '.pdb']]
* [[Calculating energy of a conformation]]
* [[Calculating molecular properties]]
* [[Calculating order parameters]]
* [[CAMSHIFT]]
* [[Setting up (CHARMM)]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths (CHARMM)]]

=== [[disconnectionDPS]] ===
Produces disconnectivity graphs from min.data and ts.data files. This is included in the Wales group public tarball.
* [[Constructing Free Energy Disconnectivity Graphs]]

=== [[DMACRYS]] ===
Package which models crystals of rigid molecules.
* [http://www.chem.ucl.ac.uk/cposs/dmacrys/index.html Home Page]
* [[DMACRYS interface]]
* [[DMAGMIN setup]]
* [[PYGMIN & DMACRYS]]

=== [[GAMESS]] ===
General ''ab initio'' quantum chemistry package.
* [https://www.msg.chem.iastate.edu/gamess/ GAMESS]

=== [[Gaussian]] ===
General purpose package for computational chemistry calculations.
* [[Running an Gaussian03 interfaced OPTIM job]]

=== [[gnuplot]] ===
Open source graphing program.
* [http://www.gnuplot.info/ gnuplot]
* [[Plotting a quick histogram in gnuplot using the raw data]]
* [[Plotting data in real time]]
* [[Linear and non-linear regression in gnuplot]]

=== [[GROMACS]] ===
Molecular dynamics package.
* [[Installing GROMACS on Clust]]
* [http://www.mdtutorials.com/gmx/ External tutorials]
* [http://www.gromacs.org/Documentation/Tutorials More external tutorials]

=== [[HiRE-RNA]] ===
High-res course-grained energy model for RNA.
* [https://pubs.acs.org/doi/10.1021/jp102497y Explanatory Paper]

=== [[latex2html]] ===
Script which converts latex documents into HTML pages.
* [https://www.latex2html.org/ Get script here]

=== [[MMTSB-toolset]] ===
Group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD with CHARMM or AMBER.
* [http://feig.bch.msu.edu/mmtsb/Main_Page Documentation]
* [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html External tutorials]
* [[Installing and setting up the MMTSB toolset]]
* [[REX (Replica EXchange MD) with the MMTSB-toolset]]

=== [[Simulations using OPEP | OPEP]] ===
OPEP is a coarse-grained force field providing a potential for proteins and RNA.
* [http://opep.galaxy.ibpc.fr/ OPEP file generator here]
* [[Biomolecules in the energy landscape framework]]

=== [[pgprof]] ===
Profiler for portland-compiled codes
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

=== [[Pymol]] ===
Molecular visualisation program.
* [https://pymol.org/2/ PyMOL]
* [https://pymolwiki.org/index.php/Main_Page PyMOL Community Wiki]
* [[loading AMBER prmtop and inpcrd files into Pymol]]
* [[producing sexy ray-traced images]]
* [[advanced colouring]]
* [[Installing python modules]]
* [[PYGMIN & DMACRYS]]
* [[path2pdb.py]] - A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
=== [[VASP]] ===
OPTIM has an interface to VASP, which is installed on CSD3. In collaboration with Bora Karasulu the interface has been updated to use VASP format POSCAR input files for both single- and double-ended optimisations and path searches. The OPTIM odata file requires a line like

VASP 'mpirun -ppn 16 -np 16 /home/bk393/APPS/vasp.5.4.4/with-VTST/bin/vasp_std > vasp.out'

POSCAR files can be visualised using ase, the Atomic Simulation Environment, which can be accessed on volkhan via

module load anaconda/python3/5.3.0

pip install ase --user

ase-gui POSCAR1.vasp &

which assumes that ~/.input/bin is in your $PATH environment variable.

=== [[VMD]] ===
Molecular visualisation program.
* [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html Documentation]
* [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html External tutorials]
* [[using VMD to display and manipulate '.pdb' files]]
* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9
* [[visualising normal modes using VMD and OPTIM]]
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[Useful .vmdrc file]]
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
* [[VMD script to annotate each frame of a trajectory]]

=== [[xfig]] ===
Open source vector graphics editor
* [https://ctan.org/tex-archive/support/epstopdf/ Convert eps to pdf]

=== [[Xmakemol]] ===
Program for visualising atomic and molecular systems.
* [https://www.nongnu.org/xmakemol/ XMakemol]

=== [[xmgrace]] ===
2D plotting tool.
* [http://exciting-code.org/xmgrace-quickstart Xmgrace]

== Theoretical/Mathematical Notes ==

* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[Ellipsoid.model]]
* [[Ellipsoid.model.xyz]]
* [[Ellipsoid.xyz]]
* [[Gencoords]]
* [[GenCoords]]
* [[GenCoords Models]]
* [[Rotamer moves in AMBER]]
* [[Thomson problem in OPTIM]]

=== Angle-axis notes ===

* [[Angle-axis framework]]
* [[Computing normal modes in angle-axis]]

=== Rigid Bodies ===

* [[Automatic Rigid Body Grouping]]
* [[Rigid body input files for proteins using genrigid-input.py]]
* [[Local Rigid Body Framework]]
* [[Local rigid body in OPTIM]]

== Useful Scripts ==
* [[perm-prmtop.py]]: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[colourdiscon.py]]: A python program for sorting input for disconnectivity graphs
* [[pdb_to_movie.py]]: A python program to create an AMH movieseg file from a PDB file
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining
* [[recommended bash aliases]]
* [[David's .inputrc file]]
* [[Useful .vmdrc file]]
* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[GenCoords]]: A fortran program to generate coarse grain building blocks and initial coords using a set of geometric models.
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
See also the SCRIPTS/ directory in the SVN repository!
* [[Computing CHARMM FF energy using GMIN, MMTSB and CHARMM]] - Computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB options.
* [[Automatic Rigid Body Grouping]]
* [[ElaborateDiff]]
* [[Parameter-scanning script]]
* [[Pdb to movie.py]]
* [[VMD script to annotate each frame of a trajectory]]

== Useful links ==
* [http://www.ch.cam.ac.uk/computing/theory-compute-clusters The Theory Compute Clusters support page]. Contains useful cluster specific information, including example job submission scripts.

* A useful website which contains AMBER (GAFF) and OPLS parameters for small molecules. http://virtualchemistry.org/gmld.php . This could save us lot of time while trying to derive parameters on our own. If you are lucky, the molecule of your interest may already be there in the existing database. The topology files are in GROMACS format but possibly can be converted into AMBER parameter files. (script anyone ?)

* The moving-domain QM/MM method developed by Victor Batista's group http://gascon.chem.uconn.edu/software. This approach can be used in the derivation of charges for large proteins and nucleic acids, where a full-fledged ONIOM based calculation is comptutationally prohibitive. It has been applied to systems like the Gramicidin ion channel and Photosystem II.

== Miscellaneous ==
* [[Animated GIF on the group website]]
* [[Backup strategy]]
* [[Chain crossing]]
* [[Computer Office services]]
* [[Computing values only once]]
* [[Decoding heat capacity curves]]
* [[Differences from Clust]]
* [[Fixing thunderbird links]]
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Intel Trace Analyzer and Collector]]
* [[LDAP plans]]
* [[Lapack compilation]]
* [[Mek-quake Queueing system]]
* [[Mek-quake initial setup notes]]
* [[New mek-quake]]
* [[Maui compilation]]
* [[Torque and Maui]]
* [[Mercurial]]
* [[Migrating to the new SVN server]]
* [[NECI Parallelization]]
* [[Optimization tricks]]
* [[Other IT stuff]]
* [[Porfuncs Documentation]]
* [[Progress]]
* [[Proposed changes to backup and archiving]]
* [[Rama upgrade]]
* [[Remastering Knoppix]]
* [[See unpacked nodes]]
* [[Tardis scheduling policy]]
* [[Zippo Sicortex machine]]
* [[Beginner's guide to working in Wales group]]

== Useful linux stuff ==

===Basics===
* [[basic linux commands everyone should know!]]
* [[piping and redirecting output from one command or file to another]] - how to save yourself hours!
* [[bash loop tricks]]
* [[bash history searching]]

===Remote access===
* [[setting up aliases to quickly log you in to a different machine]]
* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''
* [[using 'ssh-keygen' to automatically log you into clusters from your workstation]] (no more typing in your password!)
* [[mounting sharedscratch locally]]

===Find and replace===
* [[short 'sed' examples]]
* [[quick guide to awk]]
* [[short 'awk' examples]]

===File manipulation===
* [[sorting a file by multiple columns]]
* [[using tar and gzip to compress/uncompress files | using tar and bzip2 to compress/uncompress files]]
* [[conversion between different data file formats]] -'almost one-line' scripts
* [[conversion between different image file formats]] - the ''convert'' command
* [[removing an excessive number of files from a directory - when 'rm' just isn't enough]]

===Cluster queues===
* [[submitting jobs, interactively or to a cluster queue system]]
* [[identifying job on a node]] - if you need to kill only one of few running jobs
* [[a guide to using SLURM to run PATHSAMPLE]]
* [[a guide to using SLURM to run GPU jobs on pat]]
* [[interactive jobs on cluster]]

===Miscellaneous/uncategorised===
* [[installing packages on your managed CUC3 workstation]]
* [[running programs in the background]] - so you can use your shell for other things at the same time
* [[finding bugs in latex documents that will not compile]]
* [[printing files from the command line using 'lpr']]
* [[uploading non image files to the wiki]]

== Compiler Flags ==

* [[Compiler Flags]]
* [[Blacklisting Compilers]]
* [[Lapack compilation]]
* [[Pdb to movie.py]]
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

== SuSE ==

* [[Upgrading destiny]]
* [[Upgrading sword]]
* [[SuSE 10.1 workstation image]]
* [[SuSE 10.2 workstation image]]
* [[SuSE 10.3 workstation image]]
* [[SuSE 11.1]]

--[[User:adk44|adk44]] 17.00, 9 May 2019 (BST)

Beginner's guide to working in Wales group

2020-04-13T18:08:40Z

Nn320:

===How to add papers to group bib?===
*Make sure you are logged in to your workstation at the department. Whenever asked for a password, enter your admitto password.
*In your home directory create a working copy of the bib directory.
<pre>
cd ~
svn checkout https://svn.ch.cam.ac.uk/svn/wales/groups/djwpapers/bib
cd bib
svn update
</pre>
* Open the file you want to edit using vi, make desired changes and save them.
Note that bib entry for a paper can easily be obtained by googling the paper first, find the link 'cite this' somewhere, choose 'Bib Tex' option when asked to select citation manager/file format and then download it (or directly open it) to see the bib entry. For naming the keys follow the group practice as given in https://wikis.ch.cam.ac.uk/wales/wiki/index.php/Wales_Group_Conventions_when_using_LaTex
*Commit your changes with a descriptive message so that others know why you made this commit.
<pre>
svn commit -m "Your message here"
</pre>

For further details visit http://subversion.apache.org/quick-start

Beginner's guide to working in Wales group

2020-04-13T15:15:14Z

Nn320:

===How to add papers to group bib?===
*Make sure you are logged in to your workstation at the department. Whenever asked for a password, enter your admitto password.
*In your home directory create a working copy of the bib directory.
<pre>
cd ~
svn checkout https://svn.ch.cam.ac.uk/svn/wales/groups/djwpapers/bib
cd bib
svn update
</pre>
* Open the file you want to edit using vi, make desired changes and save them.
Note that bib entry for a paper can easily be obtained by googling the paper first, find the link 'cite this' somewhere, choose 'Bib Tex' option when asked to select citation manager/file format and then download it (or directly open it) to see the bib entry. For naming the keys follow the group practice as given in https://wikis.ch.cam.ac.uk/wales/wiki/index.php/Wales_Group_Conventions_when_using_LaTex
*Commit your changes with a descriptive messages so that others know why you made this commit.
<pre>
svn commit -m "Your message here"
</pre>

For further details visit http://subversion.apache.org/quick-start

Beginner's guide to working in Wales group

2020-04-13T12:27:01Z

Nn320:

===How to add papers to group bib?===
*Make sure you are logged in to your workstation at the department. Whenever asked for a password, enter your admitto password.
*In your /scratch directory create a working copy of the directory you want to make changes to.
<pre>
cd /scratch/CRSid
mkdir djwpapers
cd djwpapers
svn checkout https://svn.ch.cam.ac.uk/svn/wales/groups/djwpapers/bib
cd bib
svn update
</pre>
* Open the file you want to edit using vi, make desired changes and save them.
Note that bib entry for a paper can easily be obtained by googling the paper first, find the link 'cite this' somewhere, choose 'Bib Tex' option when asked to select citation manager/file format and then download it (or directly open it) to see the bib entry.
*Commit your changes with a descriptive messages so that others know why you made this commit.
<pre>
svn commit -m "Your message here"
</pre>
*Delete the directory you created in scratch once you are done.
<pre>
rm -rf /scratch/CRSid/djwpapers
</pre>

For further details visit http://subversion.apache.org/quick-start

Beginner's guide to working in Wales group

2020-04-13T12:25:54Z

Nn320:

===How to add papers to group bib?===
*Make sure you are logged in to your workstation at the department. Whenever asked for a password, enter your admitto password.
*In your /scratch directory create a working copy of the directory you want to make changes to.
<pre>
cd /scratch/CRSid
mkdir djwpapers
cd djwpapers
svn checkout https://svn.ch.cam.ac.uk/svn/wales/groups/djwpapers/bib
cd bib
svn update
</pre>
* Open the file you want to edit using vi, make desired changes and save them.
Note that bib entry for a paper can easily be obtained by googling the paper first, find the link 'cite this' somewhere, choose 'Bib Tex' option when asked to select citation manager/file format and then download it (or directly open it) to see the bib entry.
*Commit your changes with a descriptive messages so that others know why you made this commit.
<pre>
svn commit -m "Your message here"
</pre>
*Delete the directory you created in scratch once you are done.
<pre>
cd ..
rm -rf djwpapers
</pre>

For further details visit http://subversion.apache.org/quick-start

Beginner's guide to working in Wales group

2020-04-13T11:59:15Z

Nn320: /* How to add papers to group bib? */

===How to add papers to group bib?===
*Make sure you are logged in to your workstation at the department. Whenever asked for a password, enter your admitto password.
*In your /scratch directory create a working copy of the directory you want to make changes to.
<pre>
cd /scratch/CRSid
mkdir djwpapers
cd djwpapers
svn checkout https://svn.ch.cam.ac.uk/svn/wales/groups/djwpapers/bib
cd bib
svn update
</pre>
* Open the file you want to edit using vi, make desired changes and save them.
Note that bib entry for a paper can easily be obtained by googling the paper first, find the link 'cite this' somewhere, choose 'Bib Tex' option when asked to select citation manager/file format and then download it (or directly open it) to see the bib entry.
*Commit your changes with a descriptive messages so that others know why you made this commit.
<pre>
svn commit -m "Your message here"
</pre>

For further details visit http://subversion.apache.org/quick-start

Beginner's guide to working in Wales group

2020-04-13T11:58:22Z

Nn320: Created page with "===How to add papers to group bib?=== *Make sure you are logged in to your workstation at the department. Whenever asked for a password, enter your admitto password. *Create..."

===How to add papers to group bib?===
*Make sure you are logged in to your workstation at the department. Whenever asked for a password, enter your admitto password.
*Create a working copy of directory you want to make changes to, in your scratch.
<pre>
cd /scratch/CRSid
mkdir djwpapers
cd djwpapers
svn checkout https://svn.ch.cam.ac.uk/svn/wales/groups/djwpapers/bib
cd bib
svn update
</pre>
* Open the file you want to edit using vi, make desired changes and save them.
Note that bib entry for a paper can easily be obtained by googling the paper first, find the link 'cite this' somewhere, choose 'Bib Tex' option when asked to select citation manager/file format and then download it (or directly open it) to see the bib entry.
*Commit your changes with a descriptive messages so that others know why you made this commit.
<pre>
svn commit -m "Your message here"
</pre>

For further details visit http://subversion.apache.org/quick-start

Comprehensive Contents Page

2020-04-13T11:27:32Z

Nn320: /* Miscellaneous */

This page is designed to organise all of the pages on this wiki, as well as provide other useful links. Note that some pages may appear under more than one heading.

== Getting Started ==
[[Wales Group]] provides good step-by-step instructions. Relevant pages are:

=== Acquiring and compiling the group software ===
* [[SVN setup]]
* [[Wales Group Version control]] - to keep the code standardised.
* Theory Sector [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/SVN_Page SVN Page] - some useful general information on SVN commands.
* [[Compiling Wales Group codes using cmake]] - CMake (Cross-platform Make) allows us to compile and test the group codebase regardless of platform. This page provides crucial information how to compile using cmake.
* [[ElaborateDiff]]

=== Maintaining code health ===
* [[Jenkins CI]] - explains Jenkins, which we use to download our code and compile each of our targets with each of the compilers every night.
* https://wales-jenkins.ch.cam.ac.uk/ - log for our Jenkins tests.
* [[Branching and Merging]]
* [[Cmake interface building]]
* [[Installing python modules]]
* [[Revamping the modules system]]

=== Collaborators without access to the SVN repository ===
For licensing reasons, some code cannot be included in the Wales Group public tarball.
* http://www-wales.ch.cam.ac.uk/svn.tar.bz2 - Wales group public tarball. Includes [[GMIN]], [[OPTIM]] and [[PATHSAMPLE]].
If a collaborator has a [[CHARMM]] or [[AMBER]] licence, we do maintain separate tarballs which include the [[CHARMM]], [[AMBER]] and [[CHARMM]]+[[AMBER]] source and interfaces. These are not linked anywhere on the website and require a username ('''wales''') and password ('''group''') to download:

* [http://www-wales.ch.cam.ac.uk/CHARMM/svn.CHARMM.tar.bz2 CHARMM]
* [http://www-wales.ch.cam.ac.uk/AMBER/svn.AMBER.tar.bz2 AMBER]
* [http://www-wales.ch.cam.ac.uk/both/svn.both.tar.bz2 AMBER+CHARMM]

=== Running on Windows ===
Not particularly recommended.
* [[Running Wales Group software on Windows 7]]

== Wales Group Programs ==

=== Programs ===
* [[GMIN]]: A program for finding global minima and calculating thermodynamic properties from basin-sampling.
* [[OPTIM]]: A program for optimizing geometries and calculating reaction pathways.
* [[PATHSAMPLE]]: A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis.
* [[Pele]]: Python energy landscape explorer. A pythonic rewrite of some core functionality of GMIN, OPTIM, and PATHSAMPLE. Can be very useful for visualizing your system and for rapidly implementing and testing new ideas.

=== Curated Examples ===
* https://github.com/wales-group/examples - set of tutorials detailing how to use GMIN, OPTIM and PATHSAMPLE. Essential for beginners.
* http://www-wales.ch.cam.ac.uk/VM/Wales_Group_VM.ova - Pre-prepared teaching virtual machine. This contains the code and examples.
* https://www.virtualbox.org/wiki/Downloads - This is required if using the VM above.
* https://github.com/wales-group/examples.git - Alternatively, you can run the examples on your own machine. To get hold of the relevant files:
<pre>
git clone https://github.com/wales-group/examples.git
</pre>

== Useful Notes on Wales Group Programs and Subroutines ==
=== [[GMIN]] ===
* [[Adding a model to GMIN]] - rough outline of the subroutines that need to be changed to add a new model to GMIN
* [[Compiling Wales Group codes using cmake | Compiling GMIN using cmake ]]
* [[Selecting search parameters for GMIN]]
* [[Global optimization of biomolecules using CHARMM]]
* [[Global optimization of biomolecules using AMBER9]]
* [[Global optimization of biomolecules using AMBER9 with Structural Restraints]]
* [[Calculating binding free energy using the FSA method]]
* [[Restarting a GMIN run from a dump file]]
* [[Using the implicit membrane model IMM1]]
* [[Running a Go model with the AMHGMIN]]
* [[Running a G\=o model with the AMHGMIN]]
* [[Ligand binding-mode searches with HBONDMATRIX]]
* [[Compiling and using GMIN with QUIP]]
* [[Using GMIN and OPTIM with GPUs]]
* [[Using GMIN to generate endpoints]]
* [[Using GMIN to generate endpoints (CHARMM)]]
* [[Generating a GMIN Eclipse project]]
* [[Mutational BH steps]]
* [[Biomolecules in the energy landscape framework]]
* [[DMAGMIN setup]]
* [[Keywords]]
* [[PYGMIN & DMACRYS]]
* [[Rotamer moves in AMBER]]
* [[Python interface for GMIN/OPTIM]]

==== Scripts ====
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining

==== Useful info for coding GMIN ====
* [[Program flow]] - contains information about what the various files in GMIN do and what order they're called.
* [[amberinterface]]

==== Projects ====
* [[GMIN MOVES module]]
* [[GMIN SANITY module]]
* [[GMIN TESTS module]]
* [[CAMSHIFT]]

=== [[OPTIM]] ===
* [[Adding a model to OPTIM]] - rough outline of the subrounties that need to be changed to add a new model to OPTIM
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[visualising normal modes using VMD and OPTIM]]
* [[Compiling Wales Group codes using cmake | Compiling OPTIM using cmake ]]
* [[OPTIM/Q-Chem Tutorial]]
* [[OPTIM and PY ellipsoids tutorial]]
* [[OPTIM output files]]
* [[Minimizing a structure using OPTIM and AMBER9]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Creating movies (.mpg) of paths using OPTIM]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Debugging odd transition states in OPTIM]]
* [[Connecting two minima with a pathway]] - step by step
* [[Compiling and using OPTIM with QUIP]]
* [[Running an Gaussian03 interfaced OPTIM job]]
* [[The effect of calculating less than the maximum number of eigenvalues using ENDHESS n]]
* [[Biomolecules in the energy landscape framework]]
* [[BLJ60 example setup]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Python interface for GMIN/OPTIM]]
* [[Thomson problem in OPTIM]]
* [[Instanton tunneling and classical rate calculations with OPTIM]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[common setup problem : No Frequency Warning]]

=== [[PATHSAMPLE]] ===
* [[Adding a model to PATHSAMPLE]] - rough outline of the subrounties that need to be changed to add a new model to PATHSAMPLE
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[Compiling Wales Group codes using cmake | Compiling PATHSAMPLE using cmake ]]
* [[IMPORTANT: Using PATHSAMPLE safely on sinister]]
* [[Adding a model for PATHSAMPLE]]
* [[List of output files for PATHSAMPLE]]
* [[Using BHINTERP to find minima between two end points]]
* [[Finding an initial path between two end points (minima)]]
* [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]]
* [[Optimising a path]]
* [[Fine tuning UNTRAP]] - ensuring that it picks sensible minima
* [[Calculating rate constants (GT and fastest path)]]
* [[Calculating rate constants (SGT, DGT, and SDGT)]]
* [[Identifying the k fastest paths between endpoints using KSHORTESTPATHS]]
* [[Removing minima and transition states from the database]]
* [[Relaxing existing minima with new potential and creating new database]]
* [[Relaxing existing transition states with new potential and creating new database]]
* [[If things go wrong...]]
* [[If you lost file min.data, but still you have points.min]]
* [[path.info file is not read, causes PATHSAMPLE to die]]
* [[BLJ60 example setup]]
* [[When PATHSAMPLE finds a connected path, but using DIJKSTRA 0 fails to find the connected path]]
* [[Biomolecules in PATHSAMPLE]]
* [[Biomolecules in the energy landscape framework]]
* [[Expanding the kinetic transition network with PATHSAMPLE]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths]]
* [[Pathsampling short paths (CHARMM)]]
* [[Loading OPTIM's min.data.info files into PATHSAMPLE]]
* [[Connecting Sub-databases]]

=== [[Notes on MINPERMDIST | MINPERMDIST]] ===

=== [[Quasi-continuous interpolation for biomolecules | QCI]] ===

== Non-Group Software ==

=== [[AMBER]] ===
Molecular dynamics simulation program and associated force fields.
* [http://ambermd.org/ AMBER]
* [http://ambermd.org/tutorials/ AMBER tutorials] - recommended reading for '''ANYONE''' using AMBER!
* [[Notes on AMBER 12 interface]]
* [[Using AMBER 14 on the GPU and compute clusters]]
* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
* [[Generating parameters using RESP charges from GAMESS-US]]
* [[Simple scripts for LEaP to create topology and coordinate files]]
* [[Preparing an AMBER topology file for a protein system]] - step by step guide
* [[Setting up]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[Using Molfacture to edit molecules and add hydrogens]]
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide
* [[Symmetrising AMBER topology files]] - step by step guide for symmetrising a complex protein+ligand system
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb''
* [[Running GMIN with MD move steps AMBER]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Evaluating different components of AMBER energy function with SANDER]]
* [[Mutational BH steps]]
* [[REMD with AMBER]]
* [[Performing a hydrogen-bond analysis]]
* [[Alternatively, making the initial path with PATHSAMPLE itself]]
* [[Biomolecules in the energy landscape framework]]
* [[perm-prmtop.py]] - A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[Rotamer moves in AMBER]]
* [[Creating mismatched DNA duplex using NAB]]

=== [[aux2bib]] ===
To generate a bib file containing only the entries cited in a given .tex file from a larger bib or multiple bib files.
* [https://ctan.org/pkg/bibtools Get script here]

=== [[CamCasp]] ===
Cambridge package for Calculation of Anisotropic Site Properties
From Anthony Stone's website: 'CamCASP is a collection of scripts and programs written by Dr Alston Misquitta and myself for the calculation ab initio of distributed multipoles, polarizabilities, dispersion coefficients and repulsion parameters for individual molecules, and interaction energies between pairs of molecules using SAPT(DFT).'
* [http://www-stone.ch.cam.ac.uk/programs.html CamCASP home]
* [[CamCASP/Programming]]
* [[CamCASP/Programming/5/example1]]
* [[CamCASP/Notes]]
* [[CamCASP/Bugs]]
* [[CamCASP/ToDo/diskIO]]
* [[CamCASP/ToDo/Memory]]
* [[CamCASP/CodeExamples/DirectAccess]]

=== [[CPMD]] ===
Implementation of DFT for ''ab-initio'' molecular dynamics.
* [http://www.cpmd.org/ Home Page]
* [[CPMDInput]]

=== [[CHARMM]] ===
Molecular dynamics simulation program and associated force fields.
* [https://www.charmm.org/charmm/?CFID=65f7b3aa-8037-452a-bcd1-7583dd83a087&CFTOKEN=0 CHARMM]
* [[Generating pdb, crd and psf for a peptide sequence]]
* [[Converting between '.crd' and '.pdb']]
* [[Calculating energy of a conformation]]
* [[Calculating molecular properties]]
* [[Calculating order parameters]]
* [[CAMSHIFT]]
* [[Setting up (CHARMM)]] - step by step guide to prepare and then symmetrise a simple (protein-only) system
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Performing a normal mode analysis of a biomolecule using OPTIM (AMBER and CHARMM)]]
* [[Minimizing a structure using OPTIM and CHARMM]]
* [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]]
* [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]]
* [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]]
* [[Pathsampling short paths (CHARMM)]]

=== [[disconnectionDPS]] ===
Produces disconnectivity graphs from min.data and ts.data files. This is included in the Wales group public tarball.
* [[Constructing Free Energy Disconnectivity Graphs]]

=== [[DMACRYS]] ===
Package which models crystals of rigid molecules.
* [http://www.chem.ucl.ac.uk/cposs/dmacrys/index.html Home Page]
* [[DMACRYS interface]]
* [[DMAGMIN setup]]
* [[PYGMIN & DMACRYS]]

=== [[GAMESS]] ===
General ''ab initio'' quantum chemistry package.
* [https://www.msg.chem.iastate.edu/gamess/ GAMESS]

=== [[Gaussian]] ===
General purpose package for computational chemistry calculations.
* [[Running an Gaussian03 interfaced OPTIM job]]

=== [[gnuplot]] ===
Open source graphing program.
* [http://www.gnuplot.info/ gnuplot]
* [[Plotting a quick histogram in gnuplot using the raw data]]
* [[Plotting data in real time]]
* [[Linear and non-linear regression in gnuplot]]

=== [[GROMACS]] ===
Molecular dynamics package.
* [[Installing GROMACS on Clust]]
* [http://www.mdtutorials.com/gmx/ External tutorials]
* [http://www.gromacs.org/Documentation/Tutorials More external tutorials]

=== [[HiRE-RNA]] ===
High-res course-grained energy model for RNA.
* [https://pubs.acs.org/doi/10.1021/jp102497y Explanatory Paper]

=== [[latex2html]] ===
Script which converts latex documents into HTML pages.
* [https://www.latex2html.org/ Get script here]

=== [[MMTSB-toolset]] ===
Group of perl scripts which can be used to setup and run energy minimization, structural analysis and MD with CHARMM or AMBER.
* [http://feig.bch.msu.edu/mmtsb/Main_Page Documentation]
* [http://www.mmtsb.org/workshops/mmtsb-ctbp_2006/Tutorials/WorkshopTutorials_2006.html External tutorials]
* [[Installing and setting up the MMTSB toolset]]
* [[REX (Replica EXchange MD) with the MMTSB-toolset]]

=== [[Simulations using OPEP | OPEP]] ===
OPEP is a coarse-grained force field providing a potential for proteins and RNA.
* [http://opep.galaxy.ibpc.fr/ OPEP file generator here]
* [[Biomolecules in the energy landscape framework]]

=== [[pgprof]] ===
Profiler for portland-compiled codes
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

=== [[Pymol]] ===
Molecular visualisation program.
* [https://pymol.org/2/ PyMOL]
* [https://pymolwiki.org/index.php/Main_Page PyMOL Community Wiki]
* [[loading AMBER prmtop and inpcrd files into Pymol]]
* [[producing sexy ray-traced images]]
* [[advanced colouring]]
* [[Installing python modules]]
* [[PYGMIN & DMACRYS]]
* [[path2pdb.py]] - A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
=== [[VASP]] ===
OPTIM has an interface to VASP, which is installed on CSD3. In collaboration with Bora Karasulu the interface has been updated to use VASP format POSCAR input files for both single- and double-ended optimisations and path searches. The OPTIM odata file requires a line like

VASP 'mpirun -ppn 16 -np 16 /home/bk393/APPS/vasp.5.4.4/with-VTST/bin/vasp_std > vasp.out'

POSCAR files can be visualised using ase, the Atomic Simulation Environment, which can be accessed on volkhan via

module load anaconda/python3/5.3.0

pip install ase --user

ase-gui POSCAR1.vasp &

which assumes that ~/.input/bin is in your $PATH environment variable.

=== [[VMD]] ===
Molecular visualisation program.
* [http://www.ks.uiuc.edu/Research/vmd/current/ug/ug.html Documentation]
* [http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html External tutorials]
* [[using VMD to display and manipulate '.pdb' files]]
* [[loading coordinate files into VMD with the help of an AMBER topology file]] e.g. to visualise the results of a GMIN run using AMBER9
* [[visualising normal modes using VMD and OPTIM]]
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[Useful .vmdrc file]]
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
* [[VMD script to annotate each frame of a trajectory]]

=== [[xfig]] ===
Open source vector graphics editor
* [https://ctan.org/tex-archive/support/epstopdf/ Convert eps to pdf]

=== [[Xmakemol]] ===
Program for visualising atomic and molecular systems.
* [https://www.nongnu.org/xmakemol/ XMakemol]

=== [[xmgrace]] ===
2D plotting tool.
* [http://exciting-code.org/xmgrace-quickstart Xmgrace]

== Theoretical/Mathematical Notes ==

* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[Ellipsoid.model]]
* [[Ellipsoid.model.xyz]]
* [[Ellipsoid.xyz]]
* [[Gencoords]]
* [[GenCoords]]
* [[GenCoords Models]]
* [[Rotamer moves in AMBER]]
* [[Thomson problem in OPTIM]]

=== Angle-axis notes ===

* [[Angle-axis framework]]
* [[Computing normal modes in angle-axis]]

=== Rigid Bodies ===

* [[Automatic Rigid Body Grouping]]
* [[Rigid body input files for proteins using genrigid-input.py]]
* [[Local Rigid Body Framework]]
* [[Local rigid body in OPTIM]]

== Useful Scripts ==
* [[perm-prmtop.py]]: A python program that converts an AMBER9 topology file into one with a symmetrised potential with respect to exchange (updated for AMBER12 and ff14SB).
* [[perm-pdb.py]]: A python program that creates a ''perm.allow'' file for use with [[OPTIM]] and [[PATHSAMPLE]].
* [[path2pdb.py]]: A python program to convert ''path.info'' to ''path_all.pdb'' - you can easy visualize your path in VMD :)
* [[path2xyz.py]]: A python program to convert ''path.info'' to ''path_all.xyz''
* [[dijkstra_test.py]]: A python script to test whether the information in pairlist and ts.data connects the A and B set. (If not, PATHSAMPLE will not work without actually exiting.)
* [[extractedmin2pdb.py]]: A python program to convert ''exctractedmin'' to PDB format
* [[colourdiscon.py]]: A python program for sorting input for disconnectivity graphs
* [[pdb_to_movie.py]]: A python program to create an AMH movieseg file from a PDB file
* [[makerestart]]: A bash script to automatically set up a GMIN restart run
* [[progress]] A bash script to tell you the % completion of a GMIN job and give an estimated time remaining
* [[recommended bash aliases]]
* [[David's .inputrc file]]
* [[Useful .vmdrc file]]
* [[Density of states and thermodynamics from energy distributions at different temperatures]]
* [[GenCoords]]: A fortran program to generate coarse grain building blocks and initial coords using a set of geometric models.
* [[plotGMINms.tcl]]: a tcl script for plotting ellipsoids in VMD.
See also the SCRIPTS/ directory in the SVN repository!
* [[Computing CHARMM FF energy using GMIN, MMTSB and CHARMM]] - Computes the Charmm FF energy of the same structure. Useful for cross-validating force field settings in GMIN data file, CHARMM input file and MMTSB options.
* [[Automatic Rigid Body Grouping]]
* [[ElaborateDiff]]
* [[Parameter-scanning script]]
* [[Pdb to movie.py]]
* [[VMD script to annotate each frame of a trajectory]]

== Useful links ==
* [http://www.ch.cam.ac.uk/computing/theory-compute-clusters The Theory Compute Clusters support page]. Contains useful cluster specific information, including example job submission scripts.

* A useful website which contains AMBER (GAFF) and OPLS parameters for small molecules. http://virtualchemistry.org/gmld.php . This could save us lot of time while trying to derive parameters on our own. If you are lucky, the molecule of your interest may already be there in the existing database. The topology files are in GROMACS format but possibly can be converted into AMBER parameter files. (script anyone ?)

* The moving-domain QM/MM method developed by Victor Batista's group http://gascon.chem.uconn.edu/software. This approach can be used in the derivation of charges for large proteins and nucleic acids, where a full-fledged ONIOM based calculation is comptutationally prohibitive. It has been applied to systems like the Gramicidin ion channel and Photosystem II.

== Miscellaneous ==
* [[Animated GIF on the group website]]
* [[Backup strategy]]
* [[Chain crossing]]
* [[Computer Office services]]
* [[Computing values only once]]
* [[Decoding heat capacity curves]]
* [[Differences from Clust]]
* [[Fixing thunderbird links]]
* [[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]
* [[Intel Trace Analyzer and Collector]]
* [[LDAP plans]]
* [[Lapack compilation]]
* [[Mek-quake Queueing system]]
* [[Mek-quake initial setup notes]]
* [[New mek-quake]]
* [[Maui compilation]]
* [[Torque and Maui]]
* [[Mercurial]]
* [[Migrating to the new SVN server]]
* [[NECI Parallelization]]
* [[Optimization tricks]]
* [[Other IT stuff]]
* [[Porfuncs Documentation]]
* [[Progress]]
* [[Proposed changes to backup and archiving]]
* [[Rama upgrade]]
* [[Remastering Knoppix]]
* [[See unpacked nodes]]
* [[Tardis scheduling policy]]
* [[Zippo Sicortex machine]]
* [[Beginner's guide to working in Wales group]]

== Useful linux stuff ==

===Basics===
* [[basic linux commands everyone should know!]]
* [[piping and redirecting output from one command or file to another]] - how to save yourself hours!
* [[bash loop tricks]]
* [[bash history searching]]

===Remote access===
* [[setting up aliases to quickly log you in to a different machine]]
* [[transfering files to and from your workstation]] -using ''scp'' or ''rsync''
* [[using 'ssh-keygen' to automatically log you into clusters from your workstation]] (no more typing in your password!)
* [[mounting sharedscratch locally]]

===Find and replace===
* [[short 'sed' examples]]
* [[quick guide to awk]]
* [[short 'awk' examples]]

===File manipulation===
* [[sorting a file by multiple columns]]
* [[using tar and gzip to compress/uncompress files | using tar and bzip2 to compress/uncompress files]]
* [[conversion between different data file formats]] -'almost one-line' scripts
* [[conversion between different image file formats]] - the ''convert'' command
* [[removing an excessive number of files from a directory - when 'rm' just isn't enough]]

===Cluster queues===
* [[submitting jobs, interactively or to a cluster queue system]]
* [[identifying job on a node]] - if you need to kill only one of few running jobs
* [[a guide to using SLURM to run PATHSAMPLE]]
* [[a guide to using SLURM to run GPU jobs on pat]]

===Miscellaneous/uncategorised===
* [[installing packages on your managed CUC3 workstation]]
* [[running programs in the background]] - so you can use your shell for other things at the same time
* [[finding bugs in latex documents that will not compile]]
* [[printing files from the command line using 'lpr']]
* [[uploading non image files to the wiki]]

== Compiler Flags ==

* [[Compiler Flags]]
* [[Blacklisting Compilers]]
* [[Lapack compilation]]
* [[Pdb to movie.py]]
* [[Portland compiler fails trying to allocate an unexpectedly large amount of memory: issue with large arrays]]

== SuSE ==

* [[Upgrading destiny]]
* [[Upgrading sword]]
* [[SuSE 10.1 workstation image]]
* [[SuSE 10.2 workstation image]]
* [[SuSE 10.3 workstation image]]
* [[SuSE 11.1]]

--[[User:adk44|adk44]] 17.00, 9 May 2019 (BST)