David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 6 07:21:07 CEST 2002
On Mon, 2002-08-05 at 14:27, Christian Kandt wrote:
> Hi all!
> We got a simulation system consisting of protein, lipid, water and a
> ligand and we like to have the interaction energies written out for each
> of our four components. When included as ENERGYGRPS in the MDP-file the
> first three work fine but the ligand does not, as grompping produces:
> Fatal error: Atom 3023 in multiple Energy Mon. groups (15 and 0)
> Since our ligand is incorporated as an artificial amino acid and thus is
> part of the protein group, how is it possible to extract both the
> energies of the whole protein and a single specified residue?
> Thanks in advance,
> Christian Kandt.
You have to amke a custom index file, i.e. you make the index file using
make_ndx and then you remove your modified amino acid from the protein
and make a separate group for it. This index file has to be passed to
> "It doesn't have to be Tip-Top"
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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