AMBER Archive (2009)
Subject: Re: [AMBER] Hbond analysis: Direction of the hydrogen
From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Tue Sep 08 2009 - 14:54:22 CDT
The definition of hbond that you used in ptraj and vmd may be different. You
may check it first.
On Tue, Sep 8, 2009 at 12:45 PM, <Age.Skjevik_at_biomed.uib.no> wrote:
> 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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