[gmx-users] gcpr tutorial

Justin Lemkul jalemkul at vt.edu
Thu Jan 31 14:56:01 CET 2013

On 1/31/13 3:19 AM, Najmeh Fani wrote:
> Hello
> please help me I have a question
>   in gpcr tutorial when I run energy minimization process for inflategro with
> this command:
> grompp -f EM.mdp -c system_inflated.gro -p topol.top -o EM.tpr -maxwarn 5
> I seen an error :
> Fatal error:
> [ file strong_posre.itp, line 57 ]:
> Atom index (53) in position_restraints out of bounds (1-52).
> 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


You've either #included a position restraint file in the wrong place, or you're 
specifying atoms in the position restraint file that don't correspond to the 
[moleculetype] you're trying to restrain.



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


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