AMBER Archive (2009)

Subject: [AMBER] Help with torsions in parm99.dat file

From: Gregersen, Brent (Brent.Gregersen_at_DEShawResearch.com)
Date: Fri Mar 06 2009 - 16:44:17 CST

Can anyone comment on the following torsion parameters (found in
parm99.dat in at least amber 8-10):

HC-CT-C -O 1 0.80 0.0 -1. Junmei et
al, 1999
HC-CT-C -O 1 0.08 180.0 3. Junmei et
al, 1999
HC-CT-C -O 1 0.00 0.0 2. Explicit of
wild card X-C-CT-X

The question I have regards the last line. Is it intended that this
parameter overwrites the previous two? Or should it be included with the
two above parameters (in which case the "3" should be "-3"). Also, why
is it even necessary to list an explicit parameter of zero when a
torsion for the 4 atom types already exists?

I believe leap just ignores this parameter (or includes it with the
previous two torsions), but from the documentation on the param.dat
files http://ambermd.org/formats.html#parm.dat its not clear what the
behaviour should be in this case.

Thanks,
Brent

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