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

[Mark Abraham]

> 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 ?

AMBER force field is about as general as it comes. See the information on
the links Justin provided. Be aware that there exists GAFF (the
generalized Amber force field) for this type of problem, and there's a
tool in the AMBER suite called antechamber that helps develop such
parameters. Have a Google and read well. There are no short cuts :-)

Mark