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

Joern Lenz JLenz at zbh.uni-hamburg.de
Mon Feb 4 01:35:32 CET 2008

dear users, dear justin,
many many thanks for your fast reply.

I know that I can use any ff for which adequate parameters are set.
I calculated MD for different DNA protein complexes, but the problem is how to 
simulate the non-protein inhibitor and DNA-protein covalently linked in one 
complex, since the AMBER FF i used to use ius not parameterizes for such 
cases as far as I know.  It is exactly my problem, that i do not know how to 
parameterise this particular case and would be glad if anyone can give me a 
hint on how to do.
Has anyone an idea ? perhaps a more general ff to apply ?

thanks a million times

Re: [gmx-users] MD of DNA-protein complex AND non-protein inhibitor
Justin A. Lemkul
 Sun, 03 Feb 2008 09:46:04 -0800
Quoting jlenz <[EMAIL PROTECTED]>:

> 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 
developed for both proteins and DNA.  In terms of your ligand and how to treat
it, see here:




> any suggestions would be of great help
> thanks in advance
> greetings
> joern

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