hello everyone,<br><br>while doing grompp for prest by giving command<br>grompp -f *_md_water_prest.mdp -c *_md_water_em.gro -p *.top -o *_md_water_prest.tpr<br><br><b>i get the error</b><br>------------------------------------------------------<br>
Program grompp, VERSION 4.0<br>Source code file: toppush.c, line: 1196<br><br>Fatal error:<br>[ file posre.itp, line 8 ]:<br>Atom index (7) in position_restraints out of bounds (1-3).<br>This probably means that you have inserted topology section "position_restraints"<br>
in a part belonging to a different molecule than you intended to.<br>In that case move the "position_restraints" section to the right molecule.<br><br><b>my topology file is </b><br>; The Force Fields to be included<br>
#include "ffgmx.itp"<br><br>; Include topology<br>#include "boc.itp"<br><br><b>; Include water topology<br>#include "spc.itp"<br><br>; Include position restraint file <br>#ifdef POSRES<br>#include "posre.itp"<br>
#endif</b><br><br>#ifdef POSRE_WATER<br>; Position Restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br>
<br>[ system ]<br>; Name<br>DRG in water<br><br>[ molecules ]<br>; Compound #mols<br>DRG 1<br><br><b>but then on ur advice to the mail which i had written earlier<br>i had rearrange my top file i.e i had interchanged water topolgy and position restraint position<br>
i.e.</b><br>; The Force Fields to be included<br>#include "ffgmx.itp"<br><br>; Include topology<br>#include "boc.itp"<br><br><b>; Include position restraint file <br>#ifdef POSRES<br>#include "posre.itp"<br>
#endif<br><br>; Include water topology<br>#include "spc.itp"<br></b><br>#ifdef POSRE_WATER<br>; Position Restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>#endif<br><br>[ system ]<br>; Name<br>DRG in water<br><br>[ molecules ]<br>; Compound #mols<br>DRG 1<br>SOL 936<br><br><b>After that i get no error.<br>
tell me whether i m correct at this point<br></b><br>Bhawana<br><br>