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
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