Re: alchemical fep amber topology

From: Chris Harrison (
Date: Sat Mar 14 2009 - 08:33:48 CDT

As far as I'm aware, unless dual topology has been recently implemented, the AMBER MD code uses single topology and cannot utilize dual topology approaches. So naturally, as pointed out by Jerome and Floris, there is no corresponding way to define dual topologies in the Amber file formats and therefore if you are using Amber format files of the topology and initial coordinates then NAMD cannot do dual topology FEPs (for that format).

However, there are available converted topology and parameter files for
the Amber forcefield written in the CHARMM format, so with work it is in
principle possible to do dual topology FEPs with the Amber forcefield,
just not with the Amber file formats.


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
Floris Buelens <> writes:
> Date: Sat, 14 Mar 2009 03:53:37 -0700 (PDT)
> From: Floris Buelens <>
> To: George Madalin Giambasu <>,
> Subject: Re: namd-l: alchemical fep amber topology
> Return-Path:
> Message-ID: <>
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> Hi George,
> In principle this is absolutely fine in both released and CVS versions of NAMD - just do everything according to the tutorial, but with "amber on" and "parmfile" instead of a PSF file. However, there is as yet no equivalent to 'alchemify' for parm7 files. This is only an issue if you're working with dual topology alchemical groups that are bonded to the rest of the system (e.g. a dual topology residue definition) - for groups that aren't bonded to the rest of the system everything should work as you would expect without modifying the parm7.
> Floris
> ----- Original Message ----
> From: George Madalin Giambasu <>
> To:
> Sent: Friday, 13 March, 2009 18:55:22
> Subject: namd-l: alchemical fep amber topology
> 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

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