[gmx-users] MD of DNA-protein complex AND non-protein inhibitor

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Feb 4 10:10:06 CET 2008

To enhance Marks reply.

One way to do it could be:
Take the pdb-structure of your ligand and feed it to a QM-software (e.g. 
Gaussian). Optimize the geometry and compute the partial charges (RESP).
The bonded interaction are, as usual somewhat more tricky; maybe this 
GAFF from amber can help you with that. If not, try to find the correct 
atom types and the according bonds,angles and dihedrals.
All this is in fact really advanced MD stuff. Don't think you can do it 
by some clicking in a program. You have to read the background 
literature about parametrization and test your topologies in the best 
case against some experimental data.

Good luck

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

jlenz wrote:
> dear gromacs users,
> i used gromacs calculate MD trajectories of protein and DNA covalently 
> linked. to do so i applied the AMBER ff ports.
> afterwards i used a molecular docking tool to dock small non-protein 
> ligands into potential cavities built of the DNA-protein complex.
> now i am facing the problem, that i again want to simulate the molecular 
> dynamics of the most promising complexes of the protein-DNA complex and 
> the ligand but do not know which force field to use. additionally how 
> can i set up the parameters for the ligands?
> any suggestions would be of great help
> thanks in advance
> greetings
> joern
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