[AMBER-Developers] Dihedrals

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 14 Sep 2010 15:44:39 -0400


I have a question about the dihedrals and how they're computed in sander and
NAB. I looked through ene.f (specifically subroutine ephi) and traced some
variables, and I found what appeared to be the where the dihedral energy
term is computed (excluding all 1-4 nonbonds here). What I found is

epw(jn) = (pk(ic)+cosnp*gamc(ic)+sinnp*gams(ic))*fzi(jn)

which appears right at first glance. However, when I move over to NAB,
there's a switch block that requires the periodicity to be 1, 2, 3, 4, or 6
or it quits with a "bad periodicity" error. I don't see the equivalent of
that anywhere in sander. Am I missing something? Why the difference.

Taking this 1 step further, this limitation in NAB makes it unable to
correctly simulate some molecules built with ff99SBildn, since that force
field appears to have periodicities of 5 in 3 dihedrals:

N -CT-CT-C6 1 0.2317 0.0 -5.
C -CT-CT-C5 1 0.1042 0.0 -5.
N -C5-CT-CT 1 0.1298 0.0 -5.

I believe these will cause grief in NAB, but will they work in sander? I'm
also assuming sander and pmemd treat them identically? Is it worth
extending NAB to handle PN=5?


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER-Developers mailing list
Received on Tue Sep 14 2010 - 13:00:02 PDT
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