AMBER Archive (2006)

Subject: Re: AMBER: ptraj hbond analysis troubles

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Thu Oct 05 2006 - 14:43:37 CDT

> Okay, I had my donors and acceptors backward here, thinking of "H donor"
> instead of "electron pair donor to the H bond". So indeed you can get
> the generic designations to work, and pick up reasonable other H bonding

Yes, this is "my bad" as the saying goes.
>
> On angles, Tom clarified for me that the cutoff angle is indeed the
> value below which the donor--H--acceptor is not permitted to go, so
> specifying angle 120.0 (the default) excludes bonds where this angle is
> 0-60 degrees. Here's the confusing point. In the printout, such bond
> angles would be reported as angles in the range of 60-180 degrees (so
> the angle in the series printout has had 180 subtracted from the actual
> donor--H--acceptor angle, and 0 here is a nice linear H bond. Tom does

Actually, I think the opposite. For the hbond angle cutoff, a value of
120 means that the hbond angle has to be greater than 120,

   donor -- H -----
        ( \ ) angle2
     angle1 acceptor

180.0 is a linear hydrogen bond. In practice I either use no cutoff for
the angle (angle -1.0) or something liberal like 90.0. The cutoff angle
is angle1 in that figure above.

For some reason I cannot remember, I report the angle as
(180. - angle) or angle2 in the figure.

So, for an angle cutoff of 120, the reported angles will be 0-60.

Who knows how my convoluted mind was working when I dreamed this up as a
research prototype that we eventually released. Clearly work is necessary
to improve the manual, to show tutorials, to auto-detect lists of
donors/acceptors, to store histograms of the distances, etc.

Sorry for the further confusion.

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