[gmx-users] backbone_few_sidechain_fixed

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 18 07:32:57 CET 2011

On 18/02/2011 5:14 PM, shahid nayeem wrote:
> 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"
> #endif
>   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
> "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.

grompp has told you exactly what the problem is. See 

> 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

define = -DPOSRES is the only thing with a chance of working.


>   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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