VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jan 25 2017 - 02:19:24 CST

As far as I know, the angle is defined D-A-H, so ideally it would be zero,
so IMHO you are right, the manual is wrong.

 

Norman Geist

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
#ANG YUN MEI ELISA#
Gesendet: Mittwoch, 25. Januar 2017 01:25
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: HBonds Plugin - Hbonds criteria

 

Hi,

 

I have a question regarding the criteria for the formation of hydrogen bond
in the VMD's Hbond plugin. Is there a mistake in the manual?

 

The manual says "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)."

 

Angle D-H-A is typically obtuse. Should it be angle H-D-A instead?

 

Thanks,

Elisa