AMBER Archive (2004)

Subject: Re: AMBER: H Bonds

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed May 05 2004 - 16:18:22 CDT

> The other thing I want to ask is about the angle which is given in the
> list file. The angle given by carnal is quite different from that given by
> some other software. Can anyone through some light on this.

The angle reported by carnal is as follows:

   D-H...A

where D is donor, H is the hydrogen, and A is the acceptor - H
is the apex point of the angle. Perhaps your other software uses
a different atom as the apex?

Also, if a series of angles is treated statistically (e.g. averaged),
the correct way to do it is via 'circular statistics', and possibly
your other software does not do this. (This method allows the average
of 359 degrees and 1 degree to be 0 rather than 180.)

Bill
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