Subject: Improper dihedrals in the Amber potential

From: <[email-masked]>
Date: Fri, 14 Feb 1997 11:47:43 -0800 (PST)

I am using the Amber94 potential 
	(http://www.amber.ucsf.edu/amber/ff94.html)
	...
	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?

This info is in the documentation describing the format of the 
file involved, (http://www.amber.ucsf.edu/amber/doc/prep.doc):

> where the central atom (K) is the third atom in the improper
> and the order of the other three is determined alphabetically
> by atom type and if types are the same by atom number.

It also bears repetition in the page on deriving new parameters,
http://www.amber.ucsf.edu/amber/newparams.html, which perhaps is
the most detailed explanation of the force field terms.

Note that the rule given is arbitrary and is mainly intended to
provide uniformity; no general 'right answer' exists in the
physical sense.

	I'd be interested to know whether there is an "official" interpretation,

This is it..

Bill Ross, UCSF