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

Hi, Age,

The definition of hbond that you used in ptraj and vmd may be different. You
may check it first.
Good luck
shulin

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 Å 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 Å. My question is whether the hbond analysis takes into
> consideration the
> direction of the hydrogen?
>
> Thanks in advance.
>
> Best regards,
>
> Åge Skjevik, University of Bergen, Norway
>
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