VMD-L Mailing List
From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Tue Dec 03 2013 - 08:31:52 CST
Dear Sun YuePing -
Adv Protein Chem. 2005;72:1-38.
Potential functions for hydrogen bonds in protein structure prediction and design.
Morozov AV, Kortemme T.
Their Fig. 2.A has the histogram you need.
On 2013-12-03, at 2:45 AM, sunyeping 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? Thanks again.
> Yeping Sun
> Institute of Microbiology, Chinese Academy of Sciences
> 发件人：Axel Kohlmeyer <akohlmey_at_gmail.com>
> 发送时间：2013年12月3日(星期二) 13:31
> 收件人：孙业平 <sunyeping_at_aliyun.com>
> 抄 送：vmd-l <vmd-l_at_ks.uiuc.edu>
> 主 题：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.
> > 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.