Re: Suggestions on parameterizing a ligand to simulate in NAMD

From: Aron Broom (
Date: Mon May 20 2013 - 14:10:21 CDT

I've generally used AMBER forcefields and done ligand parameterization
using RESP server for charges and then LeAP and GAFF for the rest.

On Mon, May 20, 2013 at 2:03 PM, Peterson J <> wrote:

> Hi VMD and NAMD users,
> I'm very new to VMD and NAMD. I'm now in the process of parameterizing a
> ligand molecule. As I came across various a few web tools like paramchem,
> swissparam and so on. I have also seen VMD providing a plugin called
> Forcefield Toolkit calculating parameters using Gaussian and preparing the
> files for MD run using NAMD.
> I would like to get a few suggestion points on which one to use and the
> advantages and disadvantages over one another.
> What if I use one of the mentioned webtools instead of ffTk that use
> lengthy QM calculations to obtain the parameters?
> Thanks in advance for the suggestions.
> -Peterson

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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