[gmx-users] error in index file

[abhisek Mondal]

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
> > > --
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> >
> >
> >
> > --
> > 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*