AMBER Archive (2004)

Subject: AMBER: HBOND calculation

From: John (john.dalmaris_at_imperial.ac.uk)
Date: Mon Mar 29 2004 - 11:40:26 CST

Hello All,

I would like to calculate potential hydrogen bonds in my structure. Using
Carnal according to the manual the following command should be used:
HBOND h1 DISTANCE 3.3 ANGLE ? STATS;

Could you please tell me are the statistically preferred angles that Carnal
uses as default? Is it a single set or is it a different set for specific
hydrogen bonds under consideration? 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?

Thank you for the help.

Kind regards,

John

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