[gmx-users] position restraints and out of bounds atom index
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Mon Oct 18 17:05:18 CEST 2010
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
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.
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: asaraujo at fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.suman at 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"
> #include "proteina.gro_Protein_chain_H.itp"
> ; Include Position restraint file for chain H
> #ifdef POSRES
> #include "posre_Protein_chain_H.itp"
> #include "proteina.gro_Protein_chain_L.itp"
> ; Include Position restraint file for chain L
> #ifdef POSRES
> #include "posre_Protein_chain_L.itp"
> ; 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
> ; 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
> in a part belonging to a different molecule than you intended to.
> In that case move the "position_restraints" section to the right
> For more information and tips for troubleshooting, please check the
> 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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