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
meaningful.
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.
Thanks
francesco pietra
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Received on Wed Aug 01 2007 - 06:07:09 PDT
