[gmx-users] backbone_few_sidechain_fixed

shahid nayeem msnayeem at gmail.com
Fri Feb 18 07:14:32 CET 2011

Dear All
My protein complex has three chains A B C. I created three posre.itp
for backbone and some side chain which is not on the interface for
each of the chain. I put these in .top file as follows

;       File 'complex.top' was generated
;       By user: shahid (511)
;       On host: coe.iitd.ac.in
;       At date: Thu Feb 17 17:52:59 2011
;       This is your topology file
;       "They Paint Their Faces So Differently From Ours" (Gogol Bordello)
; Include forcefield parameters
#include "ffG43a1.itp"

; Include A-chain topologies
#include "complex_A.itp"
#include "complex_B.itp"
#include "complex_C.itp"

#ifdef POSRES
#include "posreA.itp"
#include "posreB.itp"
#include "posreC.itp"
 If I keep only one posreA.itp then grompp runs without error but if I
use all three or two posre.itp it gives following error.

Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 1275

Fatal error:
[ file posreB.itp, line 118 ]:
Atom index (968) in position_restraints out of bounds (1-966).
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.

I separated including topology and defining posres in three different
parts but even then it gives error and grompp fails. In my posre.itp
generated by genrestr I selected a group containing backbone and some
side chains.
My Idea is to keep the backbone as well as side chain of all the
residues which are not on interface fixed and allow free movement of
only interface residue and then run full MD. For above procedure I
defined define = POSRES in full.mdp
 Please suggest what should I do .
For a single chain I did MD keeping backbone fixed and allowing side
chain free movement. In my posres.itp I used a force of 2000 kj to
keep them in fixed position with option genrestr -fc.
Waiting for reply

Shahid Nayeem

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