[gmx-users] error group protein not found

[Ebert Maximilian]

Hi,

if there is a protein in your system you should have protein as standard group. Maybe you use a template mdp file in which the temperature coupling group is protein. if you have no protein in your simulation check the mdp files for tc-grps and adjust accordingly.

Max



> On Jun 3, 2015, at 3:07 PM, Victor Rosas Garcia <rosas.victor at gmail.com> wrote:
> 
> Hello,
> 
> In your command line you do not specify an index file. Maybe you need to
> generate one.  Check out usage of make_ndx.
> 
> Hope this helps
> 
> Victor
> 
> 2015-06-03 13:41 GMT-05:00 marzieh dehghan <dehghanmarzieh at gmail.com>:
> 
>> Hi every body
>> 
>> I create a covalent bond and now I want to held MD by gromacs,
>> 
>> after holding the following command : grompp -f nvt.mdp -c em.gro -p
>> topol.top -o nvt.tpr
>> 
>> I confornted to an 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.
>> 
>> 
>> please let me know how can I solve this problem.
>> 
>> I am looking forward to getting your answer
>> 
>> thanks a lot
>> 
>> 
>> --
>> 
>> 
>> 
>> 
>> *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and
>> Biophysics (IBB)University of Tehran, Tehran- Iran.*
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