[gmx-users] error in index file

[abhisek Mondal]

Location of the files:
https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU

On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan <e.jjordan12 at gmail.com> wrote:

> Can you post the gro file and the resulting index file?
>
> On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <abhisek.mndl at gmail.com>
> wrote:
>
> > Hi,
> >
> > I'm just having some issue creating index file for umbrella sampling.
> >
> > I have a ligand:
> > Group    20 (NAP) has    73 elements
> >
> > Now when I run following command:
> > gmx make_ndx -f npt.gro
> >
> > and try to add NAP for index.ndx, only 6 elements were being added.
> >
> > I don't understand the problem here.
> >
> > NAP is clearly showing is of 73 elements, but how come it is showing me 6
> > elements when added to index file ?
> >
> > Please help me out here.
> >
> > Thanks.
> >
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > 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.
> >
>
>
>
> --
> Joe Jordan
> --
> 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.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*