VMD-L Mailing List

From: yongle (yongle_at_ccms.ecnu.edu.cn)
Date: Sat Jan 02 2010 - 02:23:18 CST

Dear all,

Recently I'm using VMD to analyze H bonds. the default criterion of angle is 20 degr.
The explanation below is cited from http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/,
And in User's Guide, the explanation is the same.

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Criteria for the formation of a hydrogen bond
A hydrogen bond is formed between an atom with a hydrogen bonded to it (the donor, D) and another atom (the acceptor, A) provided that the distance D-A is less than the cut-off distance (default 3.0 Angstroms) and the angle D-H-A is less than the cut-off angle (default 20 degrees).
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But as much as I know, the normal D-H-A angle is always an obtuse, because for the ideal H bond,
D, H and A are line in a straight line, that is, the angle of D-H-A should be 180 degr.

Furthermore, I tested an snapshot. If I use the criterion 20 degr.
A H-bond with D-H-A angle of 153.74 is shown(Viewed with Mouse-->Label-->Angle).
Could any one tell me why the criterion is an acute angle?

2010-01-02

yongle
Ph. D. student
Institute of Theoretical and Computational Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
22 Hankou Road, Nanjing, Jiangsu 210093
P. R. China