[gmx-users] Error while trying position restraint

vivek sharma viveksharma.iitb at gmail.com
Thu Nov 13 10:52:52 CET 2008

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
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,
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081113/be5e8c00/attachment.html>

More information about the gromacs.org_gmx-users mailing list