Re: alchemical fep amber topology

From: Jerome Henin (
Date: Fri Mar 13 2009 - 15:24:43 CDT

Hi George,

With NAMD 2.6, you need Alchemify and a PSF file. The program CHARMM
is not needed, but you have to use its file format (typically created
using psfgen). I don't know if it is possible to define custom
nonbonded exclusions in an AMBER parmtop file in a way that NAMD 2.6
would understand. I have never tried.

If, however, you obtain and compile the current development version of
NAMD (or any future release), you won't need to worry about nonbonded
exclusions and all that sort of things. That is now taken care of


On Fri, Mar 13, 2009 at 2:55 PM, George Madalin Giambasu
<> wrote:
> Hi,
> I was wondering if there is a way to run alchemical fep simulations
> using Amber topologies (*.parm7 files) using the cvs version of namd?
> I found a post by Jerome Henin
> ( on
> the list in which it was stated that the fep setup "does not need CHARMM
> anymore", however the Alchemical FEP tutorial states that we have to use
> psf files in conjunction the alchemify program.
> Thanks in advance for any  suggestions or updates!
> George

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