AMBER Archive (2002)

Subject: Re: MM-PBSA philosophy

From: David Case (case_at_scripps.edu)
Date: Wed Mar 20 2002 - 10:10:05 CST

On Wed, Mar 20, 2002, Michal Otyepka wrote:

> "One cannot ignore intarmolecular strain energy and cannot derive the MM
> energy of the complex, the ligand and the protein from a single snapshot.

It *is* best to use three separate trajectories, but the statistical
requirements are then much more stringent. For a protein receptor, one
could make the following argument: proteins cannot accommodate very much
strain, so for some purposes it might be better to ignore the strain energy
than to try to calculate it.

Of course, you should expect that some reviewers will not accept this idea;
(some will not accept the notion of using a continuum solvent model at all.)
Certainly, using only a single trajectory represents an approximate
approach, best used for getting a qualitivative understanding of important
features of binding energetics.

...good luck...dac 

-- 

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