[gmx-users] .top file

[Bhawana Gupta]

hello everyone,

while doing grompp for prest by giving command
grompp -f *_md_water_prest.mdp -c *_md_water_em.gro -p *.top -o
*_md_water_prest.tpr

*i get the error*
------------------------------------------------------
Program grompp, VERSION 4.0
Source code file: toppush.c, line: 1196

Fatal error:
[ file posre.itp, line 8 ]:
Atom index (7) in position_restraints out of bounds (1-3).
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.

*my  topology file is *
; The Force Fields to be included
#include "ffgmx.itp"

; Include topology
#include "boc.itp"

*; Include water topology
#include "spc.itp"

; Include position restraint file
#ifdef POSRES
#include "posre.itp"
#endif*

#ifdef POSRE_WATER
; Position Restraint for each water oxygen
[ position_restraints ]
; i funct        fcx          fcy        fcz
  1   1         1000         1000       1000
#endif


[ system ]
; Name
DRG in water

[ molecules ]
; Compound        #mols
DRG                 1

*but then on ur advice to the mail which i had written earlier
i had rearrange my top file i.e i had interchanged water topolgy and
position restraint position
i.e.*
; The Force Fields to be included
#include "ffgmx.itp"

; Include topology
#include "boc.itp"

*; Include position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "spc.itp"
*
#ifdef POSRE_WATER
; Position Restraint for each water oxygen
[ position_restraints ]
; i funct        fcx          fcy        fcz
  1   1         1000         1000       1000
#endif

[ system ]
; Name
DRG in water

[ molecules ]
; Compound        #mols
DRG                 1
SOL               936

*After that i get no error.
tell me whether i m correct at this point
*
Bhawana
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081112/ede1b627/attachment.html>