AMBER Archive (2009)

Subject: [AMBER] Hbond analysis: Direction of the hydrogen

From: Age.Skjevik_at_biomed.uib.no
Date: Tue Sep 08 2009 - 14:45:19 CDT


Dear AMBER users,

I have run the ptraj hbond analysis on a couple of my simulations
using a distance cut-off of 3.5 ┼ and the default angle cut-off of 120
degrees. However, it resulted in somewhat higher % occupancies than
expected from examining the trajectory closely in VMD. In several of
the cases, the hydrogen in my secondary amine (acceptor) is oriented
away from, rather than towards, the oxygen donor most of the time. In
the hbond analysis, however, it seems that it is still treated as a
hydrogen bond as long as the distance is below 3.5 ┼. My question is
whether the hbond analysis takes into consideration the
direction of the hydrogen?

Thanks in advance.

Best regards,

┼ge Skjevik, University of Bergen, Norway

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