AMBER Archive (2004)

Subject: Re: AMBER: H Bonds

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu May 06 2004 - 13:16:11 CDT

> > The angle reported by carnal is as follows:
> > D-H...A
>
> "ANGLE
> Cutoff H-donor-acceptor angle in degrees (0 is linear)..."
> Page: 224, amber7 manual.

Sorry - I'd forgotten my own code. I think I chose that order
(in 1990 it seems) because I thought it was a standard. Does
anyone know if there is a standard for this?

> I mean to say that if the donor and acceptor groups are some distance
> apart which can form strong hydrogen bonds but the angle between them is
> not in the favourable region, will carnal show a hydrogen bond in this
> case also??

Carnal uses simple distance and angle criteria to judge whether a
hydrogen bond is present. The defaults are not an authoritative
statement on what constitutes an hbond (e.g. 1 radian is the angle
cutoff). Users should be aware of the nature of hbonding and draw
their own conclusions, setting their own criteria as needed.

Here's a page that a) seems to use the H as the apex and b) states
"due to the small energies involved, large deviations from collinearity
sometimes occur."

  http://www.ai.mit.edu/people/wang/main/node6.html

Bill
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