[gmx-users] error in index file

[Joe Jordan]

Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018
and using gmx select. Short of that, if you just run make_ndx and don't use
a selection sting you will get a group corresponding to NAP with the right
number of atoms.

On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal <abhisek.mndl at gmail.com>
wrote:

> I'm using v4.6.2
>
> $make_ndx -f npt.gro
>
> > r 306 (residue num of ligand)
> > name 24 Ligand
>
> This should do the work right ?
>
> On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan <e.jjordan12 at gmail.com> wrote:
>
> > I got a group with the right number of atoms when I tried it. What
> version
> > of gromacs are you using and what selection string are you using?
> >
> > On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal <abhisek.mndl at gmail.com>
> > wrote:
> >
> > > 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*
> > > > > --
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> > > >
> > > > --
> > > > Joe Jordan
> > > > --
> > > > Gromacs Users mailing list
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> > >
> > >
> > >
> > > --
> > > Abhisek Mondal
> > >
> > > *Senior Research Fellow*
> > >
> > > *Structural Biology and Bioinformatics Division*
> > > *CSIR-Indian Institute of Chemical Biology*
> > >
> > > *Kolkata 700032*
> > >
> > > *INDIA*
> > > --
> > > Gromacs Users mailing list
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> >
> >
> >
> > --
> > Joe Jordan
> > --
> > Gromacs Users mailing list
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>
>
> --
> 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/
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-- 
Joe Jordan