AMBER: thermodynamic data for conformers

From: Francesco Pietra <>
Date: Sun, 29 Jul 2007 10:11:11 -0700 (PDT)

With Amber9 I am now able to carry out a nearly unbiased sampling of
natural-product conformers via simulated annealing in vacuum.

I have subjected those of interest to MD in explicit water according to
Tutorial B1, sections 1-5, getting nice equilibrium throughout.

Question: Which procedures (thermodynamic integration ?) should now be best
followed to obtain as accurate as possible relative potential energies for the
conformers? I mean conformer + water or conformer all-not-water, if this is

I am considering the possibilities, though acquired experience by users can
shorted the way. These are non-polymeric molecules, though the problem would be
much the same for, say, polypeptides.


francesco pietra

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Received on Wed Aug 01 2007 - 06:07:09 PDT
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