Suggestions on parameterizing a ligand to simulate in NAMD

From: Peterson J (
Date: Mon May 20 2013 - 13:03:57 CDT

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.


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:12 CST