[gmx-users] position restraints and out of bounds atom index
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Sat Oct 16 20:41:10 CEST 2010
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 chain topologies
; Include Position restraint file for chain A
; Include Position restraint file for chain H
; Include Position restraint file for chain L
; Include water topology
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include topology for ions
[ system ]
ENVELOPE PROTEIN E; HEAVY CHAIN OF FAB 1A1D-2; LIGHT CHAIN OF FAB
1A1D-2 in water
[ molecules ]
; Compound #mols
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:
[ 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 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
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?
Alexandre Suman de Araujo
Instituto de Física de São Carlos
Universidade de São Paulo
São Carlos - Brasil
Novo Webmail IFSC
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