[gmx-users] question about gromacs

Andrew Bostick andrew.bostick1 at gmail.com
Tue Feb 4 14:39:33 CET 2014

Hi all

My system contain dopc + cholesterol + water + drug molecules.

I want to do MD simulation with position restraint on dopc and cholesterol

I used following lines to obtain posre*.itp files:

genrestr -f npt.gro -n index.ndx -o posre_dopc.itp

genrestr -f npt.gro -n index.ndx -o posre_chol.itp

My topol.top file is as follows:

; Include forcefield parameters
#include "gromos-43a1-s3_lipid.ff/forcefield.itp"

#include "cholesterol.itp"
#ifdef POSRES_chol
#include "posre_chol.itp"

#include "dopc.itp"
#ifdef POSRES_dopc
#include "posre_dopc.itp"

#include "gromos-43a1-s3_lipid.ff/spc.itp"

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

#include "drug.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
CHOL        26
DOPC       102
drg               1
SOL       4677

When I used grompp, I encountered error:

Fatal error:
[ file posre_chol.itp, line 34 ]:
Atom index (30) in position_restraints out of bounds (1-29).
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.

I check the GROMACS website at http://www.gromacs.org/Documentation/Errors.
in my opinion my topol.top file is true.

How to fix this error.

Any help will highly appreciated.

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