Since anybody helped me with this issue and I solved the problem, I'll
report the solution here to contribute with the comunity.
As I pointed in the original e-mail, the problem was the difference
between the numbering scheme of .gro file and .itp file.
I created 3 .pdb files, one for each chain and with pdb2gmx I created 3
.gro files. With these 3 .gro files I created 3 .ndx files with the
groups I'd like to apply PR and from these .ndx files I created the PR
.itp files, now with the numbering agreeing with the one of the topology
files.
The include of these PR.itp files in .top file is the same I mentioned
in the original e-mail.
With this, everything worked fine.
Cheers
**************************************************************
Alexandre Suman de Araujo *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto *
Universidade de São Paulo *
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com *
CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
**************************************************************
Em 16-10-2010 15:41, Alexandre Suman de Araujo escreveu:
Hi all
I'm trying to simulate a system with 3 chains (A, H and L).
Pb2gmx gave me 3 .itp files (one for each chain), each one with atom
number starting from 1, and a .top file with these 3 .itp included. It
gave me also a .gro file with the 3 chains numbered consecutively (the
atom number does not restart from 1 for each chain).
With this .gro file I made an index file using make_ndx with 3 groups
containing the backbone of each chain. With this index file I built 3
position restraint files with genrestr, one for each chain.
Following the instructions from website, I removed the #ifdef
POSRES/#include/#endif lines from the end of the .itp file of each
chain and added them directly in the .top file as shown below:
;
; File 'proteina.gro.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Thu Oct 14 14:22:01 2010
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.1
;
; Command line was:
; pdb2gmx -f 2R29CL_original.pdb -o protein.gro -p proteina.gro
-his -ignh
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "oplsaa.ff/forcefield.itp"
; Include chain topologies
#include "proteina.gro_Protein_chain_A.itp"
; Include Position restraint file for chain A
#ifdef POSRES
#include "posre_Protein_chain_A.itp"
#endif
#include "proteina.gro_Protein_chain_H.itp"
; Include Position restraint file for chain H
#ifdef POSRES
#include "posre_Protein_chain_H.itp"
#endif
#include "proteina.gro_Protein_chain_L.itp"
; Include Position restraint file for chain L
#ifdef POSRES
#include "posre_Protein_chain_L.itp"
#endif
; Include water topology
#include "oplsaa.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "oplsaa.ff/ions.itp"
[ system ]
; Name
ENVELOPE PROTEIN E; HEAVY CHAIN OF FAB 1A1D-2; LIGHT CHAIN OF FAB
1A1D-2 in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_H 1
Protein_chain_L 1
SOL 59
SOL 97
SOL 95
SOL 30308
NA 91
CL 97
When I run a simulation without the "define = -DPOSRES" definition in
the .mdp file, grompp runs ok. However, when I say in .mdp file to use
position restraints grompp give me the following error:
Fatal error:
[ file posre_Protein_chain_H.itp, line 334 ]:
Atom index (3221) in position_restraints out of bounds (1-3212).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right
molecule.
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
I know that this was already discussed in list but nothing described
there worked.
It is clear that the problem is due to the different numbering scheme
of the .gro file and .itp files. The .gro file does not restart the
numbering scheme when a new chain starts, on the other hand, the .itp
file of each chain starts from 1 in atom number field. Since the
position restraint file is generated based on numbering scheme of the
.gro file, in some cases (my case is one of them) the PR file refers
to a atom number that does not exists in .itp file.
I think the way to correct this was generate only one .itp file for
the 3 chains, or one .gro file for each chain and use them to create
the PR .itp files. However, I don't know how to do any of these 2
tasks using pdb2gmx.
Could anyone help me with this issue? There is any other program in
Gromacs package that I should use to fix this problem?
Best regards.
--
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