[gmx-users] genion

paloureiro at biof.ufrj.br paloureiro at biof.ufrj.br
Wed Dec 21 20:32:19 CET 2005

> 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.



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