Re: Alchemical transformations and DDG of point mutations

From: Gianluca Interlandi (
Date: Wed Dec 12 2012 - 16:24:09 CST

Dear Chris,

Thanks for the reference. I will read it in detail. In your work you
calculate DeltaG for binding affinities. What I meant was DeltaG of
folding, i.e., the free energy difference between folded and unfolded
state and how this difference changes due to a point mutation. This is
called DeltaDeltaG.

In the reference by Seeliger and De Groot they describe a method where
they calculate the DeltaG between wild-type and mutant in the folded state
and then repeat the same in the unfolded state (represented by a GXG
tri-peptide, X is the mutated amino acid). Then, by considering the
thermodynamic cycle, they calculate the DeltaDeltaG. Something similar is
done in the FEP tutorial to calculate the free hydration energy difference
between Ala-Tyr-Ala and Ala3. Seeliger and De Groot use the thermodynamic
integration (TI) method rather than FEP and run many simulations from
snapshots sampled along equilibrium simulations.

My questions are:

1) Is it better to use alchemy in NAMD in the FEP or TI mode for this type
of calculatons?

2) You describe that in each FEP calculation, 30 intermediate states were
considered. Does this mean that the progress of lambda was broken down
into 30 windows each of 150+150 ps? How many FEP simulations did you run
in total?

3) Do I need to use AlchDecouple on or off?

4) The VMD mutator plugin replaces both the wild-type and mutant side
chains such that both clash with the backbone. If this is a problem, I
might create the PDB myself and still use the PSF generated with VMD.

Sorry, lots of questions. I would appreciate any help on this!



On Wed, 12 Dec 2012, Chris Chipot wrote:

> Gianluca,
> 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 --
> earchHistoryKey= -- 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
> E-mail:
> Web:
> The light shines in the darkness, and the darkness has not overcome it.
> John 1:5.
> _______________________________________________________________________

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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