Re: AMBER: questions on mm_pbsa

From: Thomas Steinbrecher <>
Date: Sat, 21 Aug 2004 04:59:46 -0700


> My first question is about the radii to use to calculate the
> electrostatic part of solvation.
> It is clear that this choice has a great influence on the results. Is
> there any "good choice" ?

You have to take great care in selecting appropriate radii indeed. One
possible way might be to see if you can look up experimental solvation
free energies for some of your compounds and see if your set of radii
reproduces those.

> My second question is about the calculation of vibrationnal entropy with
> nmode on AMBER7.
> I have a quite big system (two monomers of 218 residues each) and this
> is far too much for the
> memory of my computers for running nmode. Is there any possibility to
> calculate this entropy
> without needing too much memory ?

What you can do is cut out only a certain region of interest, minimize it
and conduct NMA on that. This works for ligand binding studies but not if
your entire system is changing.



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Received on Sat Aug 21 2004 - 15:53:00 PDT
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