[AMBER] Analytical and empirical parametrization of dihedrals in Amber

From: Dmitry Nilov <nilovdm.gmail.com>
Date: Mon, 6 Dec 2010 11:43:56 +0300

Dear Amber community!
Learning dihedral parametrization procedure, I have wondered why
Parmscan program (Wang et al. 2001) implies systematic search
(systematically changes the values of the parameters in cartain step)
to minimize the difference between Etors(QM) and Etors(MM) instead of
analytical calculation of derivatives.
I suppose that the reason of this is that torsion parameters in
traditional amber force fields were fitted using just several
experimental (or QM) energy conformations of a molecule as reference
but not the whole torsion energy profile. So, analytically derived
parameters in this case could be unreliable to describe the whole
torsion profile correctly and thus unreliable to give the correct
geometry after MM energy minimization.
Of course, it is just my assumption), so could you educate me?

Thank in advance!
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Mon Dec 06 2010 - 01:00:03 PST
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