Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD

From: Jiawei Xu (
Date: Mon May 20 2013 - 14:11:50 CDT

Hi, Peterson,

In my experience, ffTk is very friendly to use, and the parameters
generated by ffTk show good quality in MD simulations to calculate
properties such as liquid density and heat of vaporization. No matter what
package you use, QM calculations are necessary.


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

Jiawei Xu

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