[gmx-users] .top file

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 12 12:42:40 CET 2008



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
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
========================================

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

========================================



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