Re: [AMBER] problem with MM-PBSA

From: case <>
Date: Wed, 29 Dec 2010 09:01:05 -0500

On Wed, Dec 29, 2010, Maryam Hamzehee wrote:
> Regarding your explanation " suggesting what sorts of
> interactions should be considered in understanding ligand binding. There
> are circumstances where it can be used as a quantitative tool for
> prediction, but these usually involve lots of comparisons (say in
> virtual screening) where one is looking more for trends than for
> individual results.", as far as I understand, you are referring to the
> trends of van der Waals, electrostatic energy, internal energy, and so
> on, and the way they change as the result of mutation. Did I get you
> correctly? I was wondering if you could kindly describe in detail your
> mean.

Yes, what you say is correct.

> And last point I am interested to know is about aromatic π-π stacking
> interaction. Which term(s) describes this sort of interaction in force
> field? E.g., does it get accounted for by the term dealing with the
> charge interaction?

There are no specific pi-pi-stacking terms, but the effect is often fairly
well reproduced. If you go to the mailing list archives, and search on "base
stacking" you will get many good discussions of this, such as this one:

(I know you are dealing with proteins rather than nucleic acids, but the
principles are the same.)


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Received on Wed Dec 29 2010 - 06:30:04 PST
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