[gmx-users] Error in genrestr

[RINU KHATTRI]

mark is correct

On Fri, Nov 28, 2014 at 2:11 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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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