VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 03 2013 - 01:48:13 CST

On Tue, Dec 3, 2013 at 8:45 AM, sunyeping <sunyeping_at_aliyun.com> wrote:
> Dear Alex,
> Thank you for the reply. I am using VMD to analyze the hydrogen between Asn
> and Try side chain. If I set the cutoff distance to 3.0 A, the occurrence
> rate of the hydrogen bond in my simulation trajectory between the two
> residue is 12%; but if I set the cutoff distance to 4.0, it becomes 68%. I
> need some authoritative documents about hydrogen bond science to support the
> 4.0 setting, but I haven't found it. Do you have any further suggestion?

you probably haven't search careful enough, or narrowed the search
down too much. you don't need to find an answer specific to your case,
but it would be better to find a paper explaining the principles and
how to determine/justify a suitable cutoff for both radius and angle.

axel.

> Thanks again.
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
> ------------------------------------------------------------------
> ·¢¼þÈË£ºAxel Kohlmeyer <akohlmey_at_gmail.com>
> ·¢ËÍʱ¼ä£º2013Äê12ÔÂ3ÈÕ(ÐÇÆÚ¶þ) 13:31
> ÊÕ¼þÈË£ºËïҵƽ <sunyeping_at_aliyun.com>
> ³­¡¡ËÍ£ºvmd-l <vmd-l_at_ks.uiuc.edu>
> Ö÷¡¡Ì⣺Re: vmd-l: hydrogen bond cutoff value
>
>
> On Tue, Dec 3, 2013 at 4:37 AM, sunyeping <sunyeping_at_aliyun.com> wrote:
>>
>> Dear all,
>>
>> In VMD the default cutoff value of a hydrogen bond is that the
>> donor-receptor distance is less than 3.0 angstroms, and the
>>
>> angle formed by the donor atom, the hydrogen atom, and the receptor atom
>> is
>> less than 20 degrees. Will it be acceptable if I change the distance
>> cutoff
>> into 4.0 angstroms? Thanks.
>
> acceptable for whom? or for what? and to show what? and with what
> justification?
>
> this all has little to do with VMD but the science of hydrogen bonds,
> so my suggestion is to read about this and look up how other
> scientists have answered the questions from above and then make an
> educated decision. remember, *you* have to defend the results and
> "some guy on the mailing list said it is ok" doesn't look very good at
> that time.
>
> axel.
>
>
>>
>>
>>
>> Yeping Sun
>>
>> Institute of Microbiology, Chinese Academy of Sciences
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.