Re: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA?

From: cristian obiol <>
Date: Fri, 23 Dec 2005 12:01:42 +0100

> > Is there any another factors influence the results? Thank you !
> Yes. Water! They can form (very) good h-bonds with the solute. So, just
> counting # of h-bonds does not necessarily give you accurate estimate of
> binding free energies.
> yong

Regarding this question, what do you think about the number of h-bonds with
the receptor ? they improve the binding energy or not ?, because you always
have the water molecules, and probably the h-bonds are better formed with
water than with the receptor so the energy balance would be binding
unfavourable as mmpbsa gives.

Cristian Obiol
Biological Systems Modelling and Drug Design
Research Group
University of Barcelona
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Received on Wed Jan 04 2006 - 18:16:50 PST
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