AMBER Archive (2004)

Subject: Re: AMBER: HBOND calculation

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Mar 29 2004 - 12:24:59 CST

> according to the manual the following command should be used:
> HBOND h1 DISTANCE 3.3 ANGLE ? STATS;

As far as I can tell the manual does not instruct one to set
a specific distance or angle.

> Could you please tell me are the statistically preferred angles that Carnal
> uses as default?

Per the manual, default for distance is 4.0A and default for
angle is 1 radian (~60 degrees).

> Is it a single set or is it a different set for specific
> hydrogen bonds under consideration?

It is the same for all hbonds under the HBOND specification.

> According to your experience is it
> better to use distances and angles when trying to investigate the
> statistical significance of hydrogen bond occurrence or only distances?

Note that in order to avoid using angle, you would have to
explictly specify a high angle.

Bill
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