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

Justin Lemkul jalemkul at vt.edu
Wed Sep 19 18:30:52 CEST 2012

On 9/19/12 12:27 PM, Lara Bunte wrote:
> Hello
> 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?

For whatever reason, protein chain names in [molecules] are not recognized by 
grompp, even though other [moleculetype] names are.  What you want is

tc-grps = Protein SOL

Alanine, by virtue of being a protein residue, will be recognized in the 
"Protein" default group.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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