VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Tue Dec 03 2013 - 01:45:26 CST

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 valueOn 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 otherscientists have answered the questions from above and then make aneducated decision. remember, *you* have to defend the results and"some guy on the mailing list said it is ok" doesn't look very good atthat time.axel.>>>> Yeping Sun>> Institute of Microbiology, Chinese Academy of Sciences>>-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0International Centre for Theoretical Physics, Trieste. Italy.