From: yongle (
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,
And in User's Guide, the explanation is the same.

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).

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?


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