[gmx-users] Error while trying position restraint

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 13 11:55:54 CET 2008

vivek sharma wrote:
> 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.

This exact question has been asked about three times in the last week.  Do check 
the archives before posting, often times the answers are there.

Also, grompp is telling you how to fix this.  This error message is one of the 
most explicit that Gromacs offers :)


> 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
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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