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 - 07:00:02 PDT
