[gmx-users] grompp - Group protein not found

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 7 21:41:15 CET 2012

On 8/03/2012 4:31 AM, Peter C. Lai wrote:
> 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]).

Those names can match and this error arise because this error is 
probably because the .mdp file refers to "protein" and there is no such 
group generated for the default index groups (used when no -n file is 

* make an index file with such a group and name it "protein,"
* copy $GMXLIB/residuetypes.dat to your working directory and add your 
protein residues to allow the default generated groups to understand 
your knowledge about what is a protein,
* name your [moleculetype] the same as your references to it in your 
.mdp file and [molecules] section.


> 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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