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

[Justin A. Lemkul]

Quoting jlenz <jlenz at zbh.uni-hamburg.de>:

> 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?

In theory, you could use any force field for which adequate parameters have been
developed for both proteins and DNA.  In terms of your ligand and how to treat
it, see here:

http://wiki.gromacs.org/index.php/Parameterization

http://wiki.gromacs.org/index.php/Exotic_Species

-Justin

>
> any suggestions would be of great help
>
> thanks in advance
>
> greetings
> joern
>
>
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Justin A. Lemkul
Graduate Research Assistant
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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