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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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