Difference between revisions of "Setting up"

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import>Jmc49
(New page: Before we can do anything, we need to set up our system. == Creating AMBER input files == === Using LEaP (from scratch) === If you're going to use GMIN to find conformations to conn...)
 
import>Jmc49
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<pre>
  
<pre>
−
source leaprc.ff99
 +
source leaprc.ff99SB
 
set default PBradii mbondi2
  
set default PBradii mbondi2
 
peptide = loadpdb alaphe_min1_amber.pdb
  
peptide = loadpdb alaphe_min1_amber.pdb
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</pre>
  
</pre>
   
−
The format used here is that each residue has 4 spaces in the file. To specify termini, you need to change the N-terminal ALA to '''NALA''' and the C-terminal PHE to 'CPHE', maintaining this format. Her is what it should look like:
 +
The format used here is that each residue has 4 spaces in the file. To specify termini, you need to change the N-terminal ALA to '''NALA''' and the C-terminal PHE to 'CPHE', maintaining this format. Here is what it should look like:
 
<pre>
  
<pre>
 
%FLAG RESIDUE_LABEL
 
%FLAG RESIDUE_LABEL
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This PDB file can then be used to generate a '''perm.allow''' file:
  
This PDB file can then be used to generate a '''perm.allow''' file:
 
<pre>
  
<pre>
−
~/svn/SCRIPTS/make_perm.allow/perm-pdb.py alaphe_min1_amber_ter.pdb
 +
~/svn/SCRIPTS/make_perm.allow/perm-pdb.py alaphe_min1_amber_ter.pdb AMBER
 
</pre>
  
</pre>
  +
  +
Note the new (as of commit number 22238, 10th June 2011) requirement for specification of whether we are using amber or charmm, as the numbering/residue labelling differs.
   
 
You should now have a perm.allow file :)
  
You should now have a perm.allow file :)

Latest revision as of 11:25, 29 June 2011

Before we can do anything, we need to set up our system.

Creating AMBER input files

Using LEaP (from scratch)

If you're going to use GMIN to find conformations to connect (for example with a small peptide) - and you don't care too much about the initial structure, you can generate it in LEaP. For the ALA-PHE peptide we're looking at here, the following LEaP input should do! 

source leaprc.ff99SB
set default PBradii mbondi2
peptide = sequence {NALA CPHE}
savepdb peptide alaphe.pdb
saveamberparm peptide coords.prmtop.old coords.inpcrd
quit

This LEaP script does the following line by line:

  • load the ff99SB forcefield parameters and atom types
  • set the Poisson-Boltzmann radii for atom to the mbondi2 set (appropriate for use with igb=2 and igb=5 options in AMBER)
  • create a peptide object with amino acid sequence ALA-PHE where ALA is at the N-terminus and PHE is at the C-terminus. The peptide is created linear with all bond lengths and angles set to their AMBER defaults.
  • save a PDB file called alaphe.pdb of the peptide object so we can easily visualise the initial conformation
  • save an AMBER topology file (coords.prmtop.old) and coordinate file (coords.inpcrd) for the peptide object

You can run this leap script as follows: 

tleap -f tleap.in

Using PDBs from other sources

When you first get PDBs either from a database, or another source, they often will not be using the atom naming conventions AMBER will be expecting. As a result, you need to do some preparation either manually renaming atoms, or preferably - using protonate, an AMBER program.

For this tutorial, we're going to be using a folded and unfolded structure for the dipeptide ALA-PHE. Here are the initial PDBs:

alaphe_min1.pdb 

REMARK  NALA
ATOM      1  N   ALA     1       4.690   2.524   1.502
ATOM      2 1H   ALA     1       5.123   1.608   1.471
ATOM      3 2H   ALA     1       4.064   2.608   2.285
ATOM      4 2H   ALA     1       5.478   3.159   1.619
ATOM      5  CA  ALA     1       4.023   2.813   0.213
ATOM      6  HA  ALA     1       3.141   2.178   0.136
ATOM      7  CB  ALA     1       3.567   4.278   0.132
ATOM      8 1HB  ALA     1       4.417   4.951   0.261
ATOM      9 2HB  ALA     1       3.103   4.465  -0.837
ATOM     10 3HB  ALA     1       2.836   4.479   0.916
ATOM     11  C   ALA     1       4.949   2.387  -0.927
ATOM     12  O   ALA     1       4.840   1.244  -1.353
ATOM     13  N   PHE     2       5.909   3.231  -1.323
ATOM     14  H   PHE     2       5.754   4.207  -1.120
ATOM     15  CA  PHE     2       7.293   2.871  -0.989
ATOM     16  HA  PHE     2       7.512   1.851  -1.311
ATOM     17  CB  PHE     2       8.262   3.844  -1.679
ATOM     18 2HB  PHE     2       8.096   3.798  -2.756
ATOM     19 3HB  PHE     2       8.038   4.862  -1.355
ATOM     20  CG  PHE     2       9.726   3.561  -1.399
ATOM     21  CD1 PHE     2      10.475   2.762  -2.283
ATOM     22  HD1 PHE     2      10.004   2.342  -3.160
ATOM     23  CE1 PHE     2      11.834   2.503  -2.025
ATOM     24  HE1 PHE     2      12.406   1.886  -2.704
ATOM     25  CZ  PHE     2      12.447   3.041  -0.879
ATOM     26  HZ  PHE     2      13.489   2.838  -0.676
ATOM     27  CE2 PHE     2      11.700   3.835   0.009
ATOM     28  HE2 PHE     2      12.165   4.240   0.896
ATOM     29  CD2 PHE     2      10.342   4.094  -0.251
ATOM     30  HD2 PHE     2       9.763   4.693   0.439
ATOM     31  C   PHE     2       7.386   2.911   0.540
ATOM     32  O   PHE     2       6.994   3.978   1.066
ATOM     33  OXT PHE     2       7.287   1.835   1.161
TER
END

alaphe_min2.pdb 

REMARK  NALA
ATOM      1  N   ALA     1       4.769   2.964  -0.028
ATOM      2 1H   ALA     1       4.610   1.986   0.154
ATOM      3 2H   ALA     1       3.983   3.392  -0.491
ATOM      4 2H   ALA     1       4.904   3.417   0.875
ATOM      5  CA  ALA     1       5.999   3.139  -0.824
ATOM      6  HA  ALA     1       6.830   2.724  -0.257
ATOM      7  CB  ALA     1       5.914   2.366  -2.148
ATOM      8 1HB  ALA     1       5.813   1.299  -1.945
ATOM      9 2HB  ALA     1       5.058   2.705  -2.732
ATOM     10 3HB  ALA     1       6.824   2.528  -2.726
ATOM     11  C   ALA     1       6.286   4.634  -1.024
ATOM     12  O   ALA     1       5.759   5.213  -1.967
ATOM     13  N   PHE     2       7.073   5.319  -0.182
ATOM     14  H   PHE     2       7.180   6.295  -0.410
ATOM     15  CA  PHE     2       7.613   4.889   1.130
ATOM     16  HA  PHE     2       7.722   5.785   1.741
ATOM     17  CB  PHE     2       9.033   4.298   0.978
ATOM     18 2HB  PHE     2       9.713   5.116   0.738
ATOM     19 3HB  PHE     2       9.348   3.908   1.948
ATOM     20  CG  PHE     2       9.226   3.211  -0.070
ATOM     21  CD1 PHE     2       9.116   1.852   0.281
ATOM     22  HD1 PHE     2       8.888   1.580   1.304
ATOM     23  CE1 PHE     2       9.287   0.851  -0.692
ATOM     24  HE1 PHE     2       9.205  -0.191  -0.412
ATOM     25  CZ  PHE     2       9.580   1.203  -2.021
ATOM     26  HZ  PHE     2       9.725   0.433  -2.766
ATOM     27  CE2 PHE     2       9.702   2.559  -2.375
ATOM     28  HE2 PHE     2       9.937   2.831  -3.395
ATOM     29  CD2 PHE     2       9.527   3.559  -1.401
ATOM     30  HD2 PHE     2       9.629   4.600  -1.674
ATOM     31  C   PHE     2       6.612   4.042   1.930
ATOM     32  O   PHE     2       5.489   4.562   2.089
ATOM     33  OXT PHE     2       6.759   2.807   1.993
TER
END

NOTE: from now on, I will only describe the preparation process for alaphe_min1.pdb - it is IDENTICAL for min2!

protonate (with the -k flag) reads through a PDB and replaces any hydrogen atoms it does not recognise with their AMBER equivalents. If you have AMBER installed, have set the $AMBERHOME variable and have included $AMBERHOME/exe in your $PATH - you should just be able to run it like this: 

protonate -k -i alaphe_min1.pdb -o alaphe_min1_amber.pdb

If not, and you have access to clust, you can use my version: 

clust:~csw34/AMBER/amber9/exe/protonate

Here is the output:

alaphe_min1_amber.pdb 

ATOM      1  N   ALA     1       4.690   2.524   1.502
ATOM      2  H1  ALA     1       5.123   1.608   1.471
ATOM      3  H2  ALA     1       5.478   3.159   1.619
ATOM      4  H3  ALA     1       4.064   2.608   2.285
ATOM      5  CA  ALA     1       4.023   2.813   0.213
ATOM      6  HA  ALA     1       3.141   2.178   0.136
ATOM      7  CB  ALA     1       3.567   4.278   0.132
ATOM      8 1HB  ALA     1       2.836   4.479   0.916
ATOM      9 2HB  ALA     1       4.417   4.951   0.261
ATOM     10 3HB  ALA     1       3.103   4.465  -0.837
ATOM     11  C   ALA     1       4.949   2.387  -0.927
ATOM     12  O   ALA     1       4.840   1.244  -1.353
ATOM     13  N   PHE     2       5.909   3.231  -1.323
ATOM     14  H   PHE     2       5.754   4.207  -1.120
ATOM     15  CA  PHE     2       7.293   2.871  -0.989
ATOM     16  HA  PHE     2       7.512   1.851  -1.311
ATOM     17  CB  PHE     2       8.262   3.844  -1.679
ATOM     18 3HB  PHE     2       8.038   4.862  -1.355
ATOM     19 2HB  PHE     2       8.096   3.798  -2.756
ATOM     20  CG  PHE     2       9.726   3.561  -1.399
ATOM     21  CD1 PHE     2      10.475   2.762  -2.283
ATOM     22  HD1 PHE     2      10.004   2.342  -3.160
ATOM     23  CE1 PHE     2      11.834   2.503  -2.025
ATOM     24  HE1 PHE     2      12.406   1.886  -2.704
ATOM     25  CZ  PHE     2      12.447   3.041  -0.879
ATOM     26  HZ  PHE     2      13.489   2.838  -0.676
ATOM     27  CE2 PHE     2      11.700   3.835   0.009
ATOM     28  HE2 PHE     2      12.165   4.240   0.896
ATOM     29  CD2 PHE     2      10.342   4.094  -0.251
ATOM     30  HD2 PHE     2       9.763   4.693   0.439
ATOM     31  C   PHE     2       7.386   2.911   0.540
ATOM     32  O   PHE     2       6.994   3.978   1.066
ATOM     33  OXT PHE     2       7.287   1.835   1.161
END

Now we're good to create some AMBER input using LEaP.

Now that we have a PDB using the AMBER naming conventions, we can load it into LEaP to create topology and coordinate files for the forcefield we're going to be using. For this tutorial, we'll use the ff99SB forcefield and we will be aiming to use the igb=2 GB solvent model (see the AMBER9 manual!). It is important to know which solvent model we will be using in advance as it affects how we create our initial AMBER input.

Again, assuming you have AMBER installed - you can use tleap to generate the input you need. First, create a tleap.in file containing the following: 

source leaprc.ff99SB
set default PBradii mbondi2
peptide = loadpdb alaphe_min1_amber.pdb
saveamberparm peptide coords.prmtop.old coords.inpcrd
quit

This LEaP script does the following line by line:

  • load the ff99SB forcefield parameters and atom types
  • set the Poisson-Boltzmann radii for atom to the mbondi2 set (appropriate for use with igb=2 and igb=5 options in AMBER)
  • load the alaphe_min1_amber.pdb PDB into LEaP as object peptide
  • save an AMBER topology file (coords.prmtop.old) and coordinate file (coords.inpcrd) for the peptide object

You can run this leap script as follows: 

tleap -f tleap.in

Symmetrising the AMBER topology file

To make sure that the improper dihedral angle energies are permutationally invariant, we need to run a script to symmetrise them. Firstly though, we need to modify the coords.prmtop.old file to make sure the script is able to identify termini correctly (the improper dihedrals for terminal residues are different!). In this case, it's quite easy as there are only two residues - both of which are terminal. Open up coords.prmtop.old in your favourite editor, and find the section that looks like this: 

%FLAG RESIDUE_LABEL     
%FORMAT(20a4)
ALA PHE
%FLAG RESIDUE_POINTER

The format used here is that each residue has 4 spaces in the file. To specify termini, you need to change the N-terminal ALA to NALA and the C-terminal PHE to 'CPHE', maintaining this format. Here is what it should look like: 

%FLAG RESIDUE_LABEL     
%FORMAT(20a4)
NALACPHE
%FLAG RESIDUE_POINTER

If you have the SVN repository checked-out in your home directory, you can run the symmetrisation script as follows: 

~/svn/SCRIPTS/AMBER/symmetrise_prmtop/perm-prmtop.ff03.py coords.prmtop.old coords.prmtop

Assuming that worked without errors, you can then open up the new coords.prmtop file and change the residue labels back from NALA to ALA and CPHE to PHE. That's it, you have a topology file ready to go. Just one more thing before we start running things - we need to make a perm.allow file for later.

Making a perm.allow file for later

The perm.allow file specifies which groups can be permuted when aligning endpoints of paths. For example, it ensures that all three H atoms of CH3 are treated as being the same, so CH3 rotation does not affect alignment. To make a perm.allow file, we need a PDB that includes the termini being specified. This means we cannot use the original PDB. We could in this case just change ALA to NALA and PHE to CPHE in the PDB manually, but you can do it automatically using the coords.prmtop.old file we made earlier which still has the termini specified. We do this using the ambpdb program: 

ambpdb -p coords.prmtop.old < coords.inpcrd > alaphe_min1_amber_ter.pdb

This PDB file can then be used to generate a perm.allow file: 

~/svn/SCRIPTS/make_perm.allow/perm-pdb.py alaphe_min1_amber_ter.pdb AMBER

Note the new (as of commit number 22238, 10th June 2011) requirement for specification of whether we are using amber or charmm, as the numbering/residue labelling differs.

You should now have a perm.allow file :)

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