Re: binding free energy calculation

From: Aron Broom (
Date: Mon Apr 22 2013 - 10:12:45 CDT

if you want individual residues, you'll need to do something like MM/PBSA.
You can do that manually with something like the NAMD energy plugin. If
you want it completely automatic, you might need to look into AmberTools.

On Sun, Apr 21, 2013 at 8:42 AM, yp sun <> wrote:

> Dear namd-I user,
> I want to calculation the free energy of a peptide binding to a protein
> and the energy contribution of individual residues of the peptide. I have
> finished namd simulation, could anyone help me with that? where can I find
> the scripts to realize it?
> Best regards,
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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