[gmx-users] Error in genrestr

[Mark Abraham]

On Fri, Nov 28, 2014 at 8:26 AM, Priya Das <priyadas001 at gmail.com> wrote:

> Dear All,
>
> I am working with a pentameric protein. I embedded it in DPPC bilayer and
> infalted the bilayer using inflate.gro.
>
> For minimization step i have used position restraints :
>
> genrestr -f opq_new.gro -o strong_posre.itp -fc 100000 100000 100000
>
> and have included the .itp file in all five the topology files generated
> for the protein. But i am getting constant error :
>
>
> *[ file strong_posre.itp, line 1260 ]:Atom index (1256) in
> position_restraints out of bounds (1-1255).*
>

The final part of
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
is probably applicable. You are doing something like generating one
position restraint file for all five proteins, which ranges over atom
numbers up to ~6250, but each [moleculetype] only knows about indices up to
~1255 because they are independent. Check out genrestr -h for advice.

Mark



> Please help
> --
> *Let us all join hands to save our " Mother Earth"*
> ------------------------------------------------------------------------
> Regards,
> Priya Das
> Research Scholar
> Dept. of Computational Biology and Bioinformatics,
> University of Kerala
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