AMBER Archive (2006)

Subject: Re: AMBER: entropic energy

From: David A. Case (
Date: Fri Feb 24 2006 - 10:36:49 CST

On Fri, Feb 24, 2006, Nina Fischer wrote:
> I am trying to calculate the relative binding free energy between
> protein-DNA complexes with the GB model.

A key question is how similar the complexes whose "relative" free energies
you are trying evaluate are. Binding entropies are hard to estimate, but
without knowing more about the structures you are looking at, one cannot say
whether it might be justified to assume that they are the same in two similar

Please note that what you are trying to do is quite difficult; it is certainly
beyond the "normal" scope of GB models. You might want to look at the
following paper (on protein-protein interactions) for a discussion of some of
the potential pitfalls:

%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250
%D 2004

...good luck...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to