[gmx-users] Problem with multiple Urea molecule position restraining.

karan syal karansyal86 at gmail.com
Mon Sep 14 09:00:21 CEST 2009

Dear All,

I am trying to do equilibration of 8M urea in gromacs 4.0 in a 3nm cubic
box. I created posre.itp from genpr selecting only UREA atoms to be
restrainted ( em.gro was used to generate this posre.itp)

*The error message is given below :*

 grompp -f pr.mdp -c em3.gro -p sys.top -o pr.tpr

                         :-)  G  R  O  M  A  C  S  (-:

                      GROwing Monsters And Cloning Shrimps

                             :-)  VERSION 4.0  (-:

      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                                :-)  grompp  (-:

Option     Filename  Type         Description
  -f         pr.mdp  Input, Opt!  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c        em3.gro  Input        Structure file: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.  Index file
  -p        sys.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o         pr.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file: edr ene

Option       Type   Value   Description
-[no]h       bool   no      Print help info and quit
-nice        int    0       Set the nicelevel
-[no]v       bool   yes     Be loud and noisy
-time        real   -1      Take frame at or first after this time.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
-maxwarn     int    0       Number of allowed warnings during input
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of

Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1.itp
Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1nb.itp
Opening library file /usr/local/gromacs4/share/gromacs/top/ffG43a1bon.itp
Opening library file /usr/local/gromacs4/share/gromacs/top/ff_dum.itp
Opening library file /usr/local/gromacs4/share/gromacs/top/spc.itp
Generated 279 of the 1225 non-bonded parameter combinations

Program grompp, VERSION 4.0
Source code file: toppush.c, line: 1196

Fatal error:
[ file posre.itp, line 13 ]:
Atom index (9) in position_restraints out of bounds (1-8).
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.

*My top file is : *

;       This is your topology file
;       UREA in Water t=   0.00000
; Include forcefield parameters
#include "ffG43a1.itp"

#include "spc.itp"
#include "urea.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

[ system ]
; Name
UREA in Water

[ molecules ]
; Compound        #mols
UREA               130
SOL               1149

I *guess* the error is because position restraints for all the 130 urea
molecules is not working but only for the first molecule of UREA.  ( Hence
out of bounds after 1-8.)

Can anyone please suggest a way out of this problem? i want to position
restrain all the urea molecules.

Thank you all for time,

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