[gmx-users] grompp - Group protein not found

[Mark Abraham]

On 8/03/2012 7:59 AM, Peter C. Lai wrote:
> Ahh, case sensitivity?
> Protein vs. protein?

No.

Mark

>
> On 2012-03-08 07:41:15AM +1100, Mark Abraham wrote:
>> 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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