From: Giacomo Fiorin (
Date: Thu Feb 16 2017 - 07:44:40 CST

Hello Jrhau, it all depends on whether you have a good CHARMM
topology/parameter set for those nucleic acids.

If not, NAMD implements other force fields, such as e.g. AMBER, which has
been used often for nucleic acids.

Lastly, post your questions regarding NAMD to its mailing list (this is the
one for VMD).


On Thu, Feb 16, 2017 at 3:59 AM, jrhau lung <> wrote:

> Dear VMD friends:
> Is it possible to use NAMD implemented Charmm force field to simulate
> the binding affinity between DNA or RNA with non-natural nucleic acid acid,
> such a PNA or LNA? Any suggestion and comment will be highly appreciated.
> Thanks.
> sincerely,
> Jrhau

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD