[gmx-users] grompp - Group protein not found

Peter C. Lai pcl at uab.edu
Wed Mar 7 18:31:36 CET 2012

Check the molecules section at the bottom of your top file. Each molecule 
entry there should match the corresponding name given to it in the molecule's 
own topology (the name under [moleculetype]).

On 2012-03-07 05:13:11PM +0000, Lara Bunte wrote:
> Hi
> I create a file pr.mdp for equilibrating the water around my molecule and used after that the command
> grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr
> And I got tthe error:
> Fatal error:
> Group protein 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.
> Could you explain that error to me please? How to fix it?
> Greetings
> Lara
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
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