Subject: Improper dihedrals in the Amber potential

From: Konrad Hinsen <[email-masked]>
Date: Fri, 14 Feb 1997 16:58:21 +0100

I am using the Amber94 potential (http://www.amber.ucsf.edu/amber/ff94.html)
in my own code, and I noticed one problem to which I could not find a
solution in the description of the force field file or in the original
publication on this force field: the correct interpretation of the
improper dihedral parameters.

An improper dihedral is defined by four atoms, a central one and three
other atoms bound to it. Each of the three bonds can be used to define
the intersection line of the two planes, and in the absence of special
symmetry the three angles will be different. So which one should I take?

The description file doesn't say anything on the interpretation of the
four atom types in an improper dihedral entry, but from looking at the
examples it is clear that the third atom must be the central one. By
analogy with proper dihedrals one may further assume that the bond
between the second and third atom defines the intersection line. That
settles the question except for two cases: when the first two atom
types are equal (as in CA-CA-C -OH) or undefined (as in X -X -C -O),
there are two possible interpretations, leading to different potential
energies.

I'd be interested to know whether there is an "official" interpretation,
or if not, what other people have decided to do about it.
-- 
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Konrad Hinsen                          | E-Mail: [email-masked]
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