[gmx-users] Equilibration Water around Alanin - Problem with Names

Lara Bunte lara.bunte at yahoo.de
Wed Sep 19 18:27:15 CEST 2012


I want to equilibrate water around the amino acid alanin. I guess I have no further errors up to here. 

In my pdb file of alanin stands in the first line COMPND Alanin

In my topology in the [ moleculetype ] block stands at name: 
Protein_chain_A. At the end of the topology file stands in the [ system ] block the Name: Alanin in water and in the [ molecules ] block at 
compund: Protein_chain_A and SOL.

In my pr.mdp file for this equilibration I wrote in the output control part energygrps = Protein_chain_A and in the temperature couplin part tc-grps Protein_chain_A SOL

The problem is that grompp gives me this error:
Fatal error:
Group Protein_chain_A 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.

Does this mean that I have to make an index file first that I should gave to grompp? 

I don't understand why this error occurs. GROMACS should know Alanin and should know SOL?

Thanks for helping me.

Lovely Greetings

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