Hi There, I am running a psition restraint mdrun. For the same I am selecting the part of the molecule surrounding my LIG, and restraining the rest of system for mdrun (using genpr).. As my system is protein in water, it is not allowing me to select a part of SOL for position restraint and rest of SOL allowed for movement, while doing so it gave me error like....
------------------------------------------------------- Program grompp_d, VERSION 3.3.3 Source code file: toppush.c, line: 1193 Fatal error: [ file "posre.itp", line 1986 ]: Atom index (2722) in position_restraints out of bounds (1-2626). 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. ------------------------------------------------------- where 2722 is the first SOL entry in the .gro file. And when I tried with keeping the whole water molecule moving (only the part of protein is kept on position restraint). iT runs successfully. Can somebody give an insight into the problem, or Is it not possible to divide SOL molecules for keeping a part of SOl for position restraint... I hope, I have clarified the question well.....if not please ask me further. Looking for suggestions.. With Thanks, Vivek
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
