Adk44: Created page with "=== Why you might want to use OPEP === OPEP is coarse grained force field providing a potential for proteins and RNA. It can speed up calculations significantly, particularly..."

2019-05-13T10:53:28Z

Created page with "=== Why you might want to use OPEP === OPEP is coarse grained force field providing a potential for proteins and RNA. It can speed up calculations significantly, particularly..."

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=== Why you might want to use OPEP ===
OPEP is coarse grained force field providing a potential for proteins and RNA. It can speed up calculations significantly, particularly for large systems. However, there are some drawbacks. Firstly, there is no documentation for the OPEP force field (other than publications). Secondly, we need to create the input files through the web interface [http://opep.galaxy.ibpc.fr/ here].

=== OPEP input files ===
There are six files you need from the OPEP setup.

conf_initiale.pdb contains the starting coordinates (at least for GMIN). It is a normal ''.pdb'' file, but for the fact that there is only one bead for the entire side chain. Make sure the file has the END line included, otherwise the input reading may fail.

<pre>
Protein nbevq
ATOM 1 NT LYS 1 -3.753 -6.023 1.545
ATOM 2 CA LYS 1 -3.633 -4.553 1.615
ATOM 3 LYS LYS 1 -3.283 -3.953 4.655
ATOM 4 C LYS 1 -2.353 -4.113 0.925
ATOM 5 O LYS 1 -1.593 -4.933 0.415
ATOM 6 N PHE 2 -2.103 -2.793 0.905
ATOM 7 HN PHE 2 -2.753 -2.163 1.335
ATOM 8 CA PHE 2 -0.923 -2.243 0.275
ATOM 9 PHE PHE 2 -0.383 -3.513 -1.945
ATOM 10 C PHE 2 -0.893 -0.733 0.395
ATOM 11 O PHE 2 -1.793 -0.133 0.965
ATOM 12 N PHE 3 0.157 -0.113 -0.145
ATOM 13 HN PHE 3 0.877 -0.653 -0.605
ATOM 14 CA PHE 3 0.307 1.327 -0.095
ATOM 15 PHE PHE 3 -0.463 2.267 2.215
ATOM 16 C PHE 3 1.587 1.777 -0.795
ATOM 17 O PHE 3 2.337 0.947 -1.305
ATOM 18 N GLU 4 1.827 3.087 -0.805
ATOM 19 HN GLU 4 1.177 3.727 -0.375
ATOM 20 CA GLU 4 3.017 3.637 -1.435
ATOM 21 GLU GLU 4 3.477 2.437 -3.885
ATOM 22 C GLU 4 3.047 5.157 -1.315
ATOM 23 OT GLU 4 2.137 5.757 -0.745
ATOM 24 OXT GLU 4 3.977 5.797 -1.795
END
</pre>

The cutoffs.dat, ichain.dat and scale.dat as well as parametres.list and parametres.top are files containing the setup and details of the force field parameters.

ichain.dat contains all fragments of the system.
<pre>
1
1 24
</pre>

scale.dat contains the scaling information for the potential.
<pre>
1 2.323
2 2.366
3 2.412
4 1.750
5 2.426
6 1.988
.
.
.
</pre>

cutoffs.dat contains the cut offs for the potential.
<pre>
1840.00d0 1600.0d0
258.75d0 225.0d0
74.60 64.0d0
258.75d0 225.0d0
</pre>

parametres.top is an AMBER style topology file.
parametres.list contains details for the side chain beads.
<pre>
LYS 8 8
PHE 6 6
PHE 6 6
GLU 17 17
3 LYS 1 9 PHE 2 -0.010 6.473 31
3 LYS 1 15 PHE 3 -0.110 6.473 5
3 LYS 1 21 GLU 4 0.870 6.111 211
9 PHE 2 15 PHE 3 -0.010 6.660 31
9 PHE 2 21 GLU 4 -0.340 6.298 86
15 PHE 3 21 GLU 4 -0.010 6.298 31
-999
0
4
</pre>

Additional parameters can be set through OPEP_params.
<pre>
use_qbug #turn on debug options for the force field
Potential_Scaling_Factor 1.2 #scaling of the force
Ion_Pair_Potential #use ion pair control
Ion_Pair_Scaling 1.2 #scaling for ion pairs
Periodic_Boundary_Condition 100.0 #turning PBC on with box length 100.0
PDB_center_of_mass #centre pdb files for PBC
RANDOM_SEED 89302123 #integer for random seed generator
usextc #use xtc format, not pdb
</pre>

=== Running GMIN ===
All that is needed for GMIN is the above files, a OPEP executable, and a data file, e.g.:
<pre>
SLOPPYCONV 1.0D-3
TIGHTCONV 1.0D-6
TRACKDATA
CENTRE
MAXERISE 1.0D-2
MAXIT 50000 50000
UPDATES 100
MAXBFGS 0.1
SAVE 500
STEPS 250000 1.0
STEP 0.1D
RADIUS 100
EDIFF 0.02
DUMPSTRUCTURES
RANSEED 20301057
TEMPERATURE 1.3
DUMPINT 10000
GROUPROTATION 2
OPEP PROTEIN
</pre>

If you use DUMPSTRUCTURES, GMIN will save the minima as .pdb and start files. FEBH, BHPT, GROUPROTATIONS and GENRIGID should all work with OPEP.

=== Running OPTIM ===
In addition to the files outlined above and odata, OPTIM needs a start file (and potentially a finish file for DNEB) and a perm.allow file.
The start and finish files are just the xyz coordinates. The perm.allow file simply contains a 0, i.e. there are no atoms to swap.

=== OPEP interface code ===
This section gives a brief overview over the changes/additions to the code for the OPEP interface.

The key file is opep_interface.F90. It contains the routine to get the number of atoms (OPEP_GET_ATOMS), which is called from getparams (OPTIM) and countatoms (GMIN), and the initialisation (OPEP_INIT). The initialisation calls DEFINITIONS(), which is in the file read_parameters.f90 that reads the OPEP_params file. We do not call the read routines for MD or ART parameters. md_initialise.F90 is called through INITIALISE. Here the potential is initialised, using protein-2006.f and RNS-2006.f. This is were all the input files are read. In md_initialise.F90 we commented out the temperature, restart and thermostat initialisation, as we do not need these.
Once these routines are finished, we have internal variables for the atom masses and coordinates, which are passed on to the main body of the program.

After this we use calls to OPEP_ENERGY_AND_GRADIENT and OPEP_NUM_HESS from potential to get all information we need to run the programs.
All output is handled as per usual and before we finish the programs we call OPEP_FINISH to deallocate all the memory.

=== Generating HiRE-RNA files ===

==== HiRE-v3 ====

===== From full-atom to coarse-grained =====

use the script in the svn, under scripts/OPEP/FA2CG:

python FA2CG.py full_atom.pdb > coarse_grained.pdb

==== HiRE-v4 ====

===== Generate parameters =====

Download and build the code at https://github.com/tc427/HiRE_generator

run the HiRE_parm executable on your pdb file.

Simulations using OPEP - Revision history

Adk44: Created page with "=== Why you might want to use OPEP === OPEP is coarse grained force field providing a potential for proteins and RNA. It can speed up calculations significantly, particularly..."