[gmx-users] grompp error

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 25 09:17:34 CET 2011

On 25/11/2011 7:09 PM, yp sun wrote:
> Dear Sir'
> When I ran the grompp as following
> grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
> a error information appeared:
> Program grompp, VERSION 3.3.1
> Source code file: readir.c, line: 789
> Fatal error:
> Group Ptotein not found in indexfile
> Maybe you have non-default goups in your mdp file, while not using the 
> '-n' opti on of grompp.
> In that case use the '-n' option
> I don't know which file "Group Ptotein" is in and where I should make 
> change.
> Can you help me? Thanks in advance.

You have referred to this group somewhere in your .mdp file, probably in 
error for "Protein". grompp went looking in the index file (possibly 
generated by default) and was confused when it didn't find what you told 
it was there to be found.

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