Have a look at the manual and search the mailing list.
You want to simulate a not recognized/parameterized molecule. Therefore
you have to implement the parameters. How thats done can be found e.g.
in the wiki.
regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
serdar durdagi wrote:
Dear all,
I am trying to make MD simulation of fullerene derivatives with HIV
protease..When I try to convert merged pdb file of protein+ligand to gmx
file, using forcefields like G43a1 it gave error message as residue
'lig' not found in residue topology database.
Is anybody knows which parameters in ff should I change?
Kind Regards,
Serdar
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