Re: How to calculate Binding Free energy in NAMD

From: Chris Chipot (
Date: Sat Jun 18 2011 - 07:51:20 CDT

Dear Jianing,

the answer to your question can be found in the free-energy perturbation
tutorial available from

Chris Chipot

On 6/18/11 1:00 AM, jnsong wrote:
> Dear all,
> Recently, I've done a simulation of protein-ligand complex using NAMD
> and CHARMM force field. and I want to get binding free energy of my
> system.
> As much as I know, In AMBER, MM-PBSA can help to get binding free
> energy, but I have no idea about how to do this in NAMD.
> Could you please tell me where can I get such information?
> Jianing

Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews                                 Phone: (217) 244-5711
Urbana, Illinois 61801                            Fax:   (217) 244-6078
The light shines in the darkness, and the darkness has not overcome it.
                                                               John 1:5.

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