Re: Benzene PSF

From: Chris Harrison (
Date: Wed Apr 29 2009 - 19:29:25 CDT


It's actually not an issue of whether or not NAMD will treat it properly but
whether or not the forcefield contains parameters for the molecule you wish
to simulate. NAMD uses forcefield parameters, specified by the user, in
order to perform simulations. There are several standard forcefields:

For the CHARMM forcefield see

For the AMBER forcefield see

NAMD is able to use both the CHARMM and AMBER forcefield, as well as that
used in GROMACS, OPLS.

To build a protein structure file of benzene, you would want to use the
Molefacture plugin in VMD ( to build
your benzene structure. If you wish to then simulate it you would use NAMD

To begin, I suggest looking at our tutorials which quickly teach you to use
VMD and NAMD ( The beginning
two initial tutorials for VMD and NAMD are available at:


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Wed, Apr 29, 2009 at 7:04 PM, Matt Krems <> wrote:
> Hello,
> I am trying to generate a protein structure file for benzene. It seems
> pretty uncommon to look at structures this small in NAMD. Does anyone know
> how to do this, and if so does NAMD actually treat such small molecules
> accurately?
> Thanks,
> Matt

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:41 CST