Re: FEP/binding free energy difference WT vs Mut

From: Jerome Henin (
Date: Fri Feb 13 2009 - 18:08:24 CST

Dear Luis,

Yes, the thermodynamic cycle you designed is correct. Just in case, I
will add that in the dissociated state (computing deltaG2), there is
no need to include the unbound DNA in the actual simulation, as it
should not be interacting with the protein anyway.
Now let me try to answer your specific questions:

1) If you can afford it, yes, it is better to use PBC with PME.
However, in some cases, using a solvent bubble may be an acceptable
simulation environment. This is not my field of expertise, so I leave
it to others to comment on this if they want to.

2) If you don't use PME, there is no need to keep the system globally
neutral (see point 1). It you do, what I would recomment is having a
chloride counterion vanish (or a sodium appear) while the arginine
disappears. Ideally this counterion should have a positional restraint
("constraint" in NAMDese) to keep it somewhere in bulk solution.

3) You can obtain individual free energy contributions if you use the
TI implementation currently available in the development version of
NAMD (CVS). I would recommend that version in any case, as in contains
many improvements to the code in general and free energy calculations
in particular.


On Fri, Feb 13, 2009 at 5:43 PM, Luis Cunha <> wrote:
> Dear NAMD users,
> I need your advice. I use NAMD to study ligand binding to my protein, but so
> far I've only been interested in conformation changes, not energies. I need
> advice with the following problem:
> I have an xray structure of a protein (actually a domain of the protein)/DNA
> complex. In this complex, an arginine makes a Hbond with a specific DNA
> base. We've found patients with a specific genetic disease who have a
> mutation (Arg to Cys) of this very arginine. Obviously this mutation has
> profound effects in the way the protein interacts with the DNA, hence it
> causes a disease. I'm hypothesizing that the Hbond removal in the mutant
> severely affects the binding capacity. An assay is being developed by
> someone else to test this in vitro. Meanwhile, I would like to estimate the
> difference in the binding energy between the mutant and wild type proteins.
> Please let me know if I got this correctly: What I need is a thermodynamic
> cycle:
> deltaG1
> WT-DNA ---------> WT + DNA
> | deltaG4 | deltaG2
> | |
> MUT-DNA --------> MUT + DNA
> DeltaG3
> And the deltadeltaG (the difference in free energy of binding between the
> mutant and the wild type) that I'm interested in would be given by
> subtracting deltaG4 from DeltaG2. These 2 deltaGs would be calculated in
> two alchemical FEP/MD experiments.
> 1) If this concept is correct, should I do the simulation in solvated
> systems, with PBC, PME?
> 2) since the positive charge of the arginine disappears, I guess I need a
> ion to appear in lambda=1?
> 3) is it possible to evaluate the individual contributions to the free
> energy difference? (electrostatic, VdW)
> thank you in advance to any help provided,
> Luis

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