AMBER Archive (2009)

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

From: Age.Skjevik_at_biomed.uib.no
Date: Tue Sep 08 2009 - 16:56:50 CDT

Hi,

Thank you for the fast reply. Actually, I haven't done hydrogen bond
analyses in VMD. I have just looked visually at the direction of the
hydrogen relative to the donor and acceptor in certain intervals for
which the ptraj hbond has calculated very high % occupancies.

Best regards,

Åge

Siterer Shulin Zhuang <shulin.zhuang_at_gmail.com>:

> 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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