[gmx-users] Problems with a three domain protein in a membrane

"Dr. Ramón Garduño-Juárez" ramon at fis.unam.mx
Thu Mar 24 20:01:27 CET 2011

Dear all,
Dear Justin,

We have been working on setting up an MD experiment in which our system 
is made of three separate domains of a protein embedded in a DMPC 
bilayer surrounded by water.

We have generated a PDB file in which our three domains are labeled as 
A, B and C (in the column corresponding to the chain identifiers). Our 
system is labeled "mod", Chain A has 342 atoms, Chain B has 289 atoms 
and Chain C has 715 atoms. Somehow these identifiers are lost when we 
use pdb2gmx.

We have gone as far as Step Three of Justin's tutorial. It is here were 
we have encountered a problem.

The steps we have performed previously without trouble are:

$ cat  mod_newbox.gro  dmpc_whole.gro >  system.gro
$ genrestr  -f  mod_newbox.gro  -o strong_posre.itp  -fc  100000  
100000  100000
$ perl inflategro.pl  system.gro  4  DMPC  14  system_inflated.gro  5  

When we wish to perform a minimization of the system via

$ grompp  -f  minim_inflo.mpd  -c  system_inflated.gro  -p  
topol_inflo.top  -o  em_system_inflated.tpr

the following error appears:

Program grompp_d, VERSION 4.5.3
Source code file: toppush.c, line: 1526

Fatal error:
[ file strong_posre.itp, line 720 ]:
Atom index (716) in position_restraints out of bounds (1-715).
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.

The topol_inflo.top file contains the following instructions:

; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRES
#include "posre_Protein_chain_A.itp"

#include "topol_Protein_chain_B.itp"
#ifdef POSRES
#include "posre_Protein_chain_B.itp"

#include "topol_Protein_chain_C.itp"
#ifdef POSRES
#include "posre_Protein_chain_C.itp"

; Strong position restraints for InflateGRO
#include "strong_posre.itp"

; Include DMPC chain topology
#include "dmpc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000

; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_B     1
Protein_chain_C     1
DMPC              128


1) Do you see any problem in the topol_inflo.top setup?

2) Do we need to create a strong_posre.itp for each chain?

Looking forward to hear your comments...

Ramon Garduno

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