Re: Protein ligand simulation Tutorial

From: Chris Chipot (
Date: Wed Feb 29 2012 - 08:07:08 CST


calculating standard binding free energies for protein-ligand complexes
can require several days of number crunching. This is not what tutorials
are designed for. The free-energy perturbation tutorial proposes an
that tackles the question of standard binding free energies using a much
simpler host-guest complex, namely an ion binding a crown ether. Once
you get some feeling on how these calculations are done, transposing to
a real protein-ligand complex should not be too difficult.

Chris Chipot

On 2/29/12 1:47 PM, sai nitin wrote:
> Hi all,
> I recently started working on Molecular Dynamics simulation using NAMD
> I wanted to do Protein ligand simulation and compute binding free
> energies can any body suggest any tutorial.
> Thanks in advance
> --
> Sainitin D

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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