[gmx-users] Reg fatal error

[Mark Abraham]

On 6/02/2012 8:31 PM, RAMYA NAGA wrote:
> Dear friends,
> iam doing protein-ligand dynamics..iam getting the error like this
>
> Group Protein_JZ4 not found in index file.
> Group names must match either [moleculetype] names
> or custom index group names,in which case you
> must supply an index file to the '-n' option of grompp.
>

You need to provide us with at least your command line that generated 
the error for us to have any chance of understanding your context.

Presumably you have used an .mdp file with grompp that references a 
custom index group, but not supplied a definition for that custom index 
group in an http://www.gromacs.org/Documentation/File_Formats/Index_File.

Mark