Bhawana Gupta wrote:
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
*
Well, assuming the posre.itp corresponds to the molecule in "boc.itp," then yes,
you are correct. Position restraint files must be #included under the
corresponding molecule type definition, so including it after spc.itp would mean
it is being applied to water, not your molecule.
Are you sure you want to be using ffgmx? It has long been considered
deprecated. The Gromos96 force fields are more recent...
-Justin
Bhawana
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
