[gmx-users] grompp - Group protein not found

[Lara Bunte]

Hi

I want to solve my problem by creating an index file but I did not understand what I have to write in this file. I read the content in this link:

http://manual.gromacs.org/online/ndx.html

but I can't apply this to my problem. Could you please help?

Thanks
Greetings
Lara






----- Ursprüngliche Message -----
Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
CC: 
Gesendet: 21:41 Mittwoch, 7.März 2012
Betreff: Re: [gmx-users] grompp - Group protein not found

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 supplied).

Either
* 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.

Mark

> 
> 
> 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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