[gmx-users] genion

[Tamas Horvath]

Ah, thanks!

On 12/21/05, paloureiro at biof.ufrj.br <paloureiro at biof.ufrj.br> wrote:
>
>
> > I've get the following error using grompp
> >
> > Fatal error: Group Protein_A not found in indexfile.
> > Maybe you have non-default goups in your mdp file, while not using the
> '-n'
> > option of grompp
> >
> > ********
> > I'm not quite sure what index file it is trying to use, or why is there
> any
> > problem...
>
> It is using the file index.ndx. Probably it has only standard groups
> (protein,
> c-alpha, SOL etc.)
> You have to run:
>
> make_ndx -f your_protein.gro -o your_protein_index.ndx
>
> Inside it, you have to create  Protein_A and Protein_B groups.
>
> Then you run grompp using also the -n  your_protein_index.ndx option.
>
> Regards.
>
> Pedro.
>
>
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