VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jul 09 2009 - 19:07:56 CDT

Hi Sasha,
you need to distinguish between the force field and MD program that
you're using. NAMD can be used with the charmm, OPLS, or amber force
fields (among others). Antechamber lets you get parameters easily for
use with the amber force field, so if you want to use the amber force
field, you can just use antechamber (there's an interface for it in the
molefacture plugin). If you want to use the charmm force field, you'll
need to use paratool to get your parameters, which does require Gaussian
or GAMESS. Please note that the latter is freely available (although I
forget whether the gamess interface in paratool is finished -- perhaps
Jan can comment).
Best,
Peter

Sasha Buzko wrote:
> Hi all,
> I need to run MD of several protein-ligand complexes, and I wonder if
> there is a general purpose compound parameter preparation tool. I did
> see a parameterization interface included with VMD, but it requires
> Gaussian/GAMESS (which we don't have).
> For use with Amber, I could do it with antechamber. Is there anything
> similar that could be used to get compound parameters for NAMD?
>
> Thanks for your help
>
> Sasha
>
>