From: chandrakala gowda (chandrakala.gowda_at_gmail.com)
Date: Tue Dec 03 2013 - 07:40:29 CST

Dear sunyeping,

There are plenty of articles published on hydrogen bonds.

Just make a simple SCOPUS or WEB OF KNOWLEDGE search for articles and reviews on hydrogen bonds

One such example is

Thomas Steiner. (2002). The hydrogen bond in the solid state. Angewandte Chemie International Edition, 41(1), 48C76.

best wishes

Chandrakala

On Dec 3, 2013, at 8:48 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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
>>
>>
>> ------------------------------------------------------------------
>> ˣAxel Kohlmeyer <akohlmey_at_gmail.com>
>> ʱ䣺2013123(ڶ) 13:31
>> ռˣҵƽ <sunyeping_at_aliyun.com>
>> ͣvmd-l <vmd-l_at_ks.uiuc.edu>
>> ⣺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.
>