Thank you for the help.
On Sat, Sep 8, 2012 at 9:38 AM, David A. Case <case.biomaps.rutgers.edu>wrote:
> On Sat, Sep 08, 2012, shomesankar bhunia wrote:
>
> > i am trying to run a MD simulation of a protein and ligand complex using
> > NAMD. I have optimized the ligand structure using GAMESS and i have done
> > RESP charge derivation using the RED-vIII.5 tools. Now i have to do
> > forcefield assignment using GAFF with AMBER tools. Can anybody please
> give
> > me an idea how to do that? If anyone can source me a tutorial that will
> be
> > helpful.
>
> Please start with tutorial B4 (at http://ambermd.org).
>
> > i also have a query that how suitable is AMBER forcefield
> > parameterization to be used in NAMD?
>
> NAMD can run simulations with several force fields. See the links on
> "Using
> the Amber force field in NAMD" at the Amber web page. It's not hard, but
> you
> have to be careful to get all the settings right.
>
> ....dac
>
>
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Received on Sat Sep 08 2012 - 09:00:02 PDT
