[gmx-users] Error in genrestr

[Priya Das]

Thank U to both.....It worked. i created separate . itp for each cain.

On Fri, Nov 28, 2014 at 2:15 PM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> 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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



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