Re: Alchemical transformations and DDG of point mutations

From: Chris Chipot (
Date: Wed Dec 12 2012 - 15:02:02 CST


there are evidently several references in which free-energy differences
arising from point mutations have been carried out with NAMD. Being
too lazy to look up for references, I will merely self-advertise our latest
paper on H1N1 neuraminidase --
-- and will let you do your own homework ;-)

If you are interested in calculating such free-energy differences yourself,
the easy road is to use the VMD plugin mutator, to define your dual
topology, run your simulation with NAMD and use the VMD plugin
parsefep for the post-treatment, notably to get a BAR estimator of
the free energy. Note that most of this stuff is documented in the FEP
tutorial available at

Chris Chipot

On 12/12/12 2:22 PM, Gianluca Interlandi wrote:
> Dear NAMD list,
> I was wondering whether there is any published work where NAMD and
> alchemical transformations were used to calculate differences in
> DeltaG due to point mutations in globular proteins.
> I found a similar thing done with gromacs:
> I wished I could find something similar done with NAMD.
> Thanks!
> Gianluca
> -----------------------------------------------------
> Gianluca Interlandi, PhD
> +1 (206) 685 4435
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

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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