AMBER: Entropy in MM_PBSA

From: Sergey Samsonov <>
Date: Mon, 20 Aug 2007 17:01:37 +0200


I'm studying the binding of the receptor (~200 aa) with ligands (5 aa),
and my aim is to calculate the binding energy in the simulation. As for
MM-PBSA part everything works without any problem. I'd like to ask for
advice related to entropy component of binding energy. Following the
tutorial (A3: MM-PBSA) on the AMBER official site, it seems that
entropic contribution could be neglected. Indeed, it seems not possible
to calculate the entropy using NMODE tool since it needs extremely
expensive calculations (moreover it gives segmentation fault because of
memory problems, which as I found, also was once mentioned and answered
at the Mailing List). So I tried PCA with 'therm' option but it seems
that the calculations are also too demanding even for small number of
frames (though without segmentation faults now). Is there any other way
to calculate the entropies of binding? Or maybe to obtain the
quantitative proof that neglecting the entropies doesn't crucially
influence the calculations? Since the final aim is to compare
ln(Kbinding) with the binding energies, there would be no problem in
neglecting entropies if for all the complexes the entropic component
approximately the same or differs in the range of the data deviation a

Thank you in advance!

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Received on Wed Aug 22 2007 - 06:07:22 PDT
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