VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Dec 05 2013 - 07:10:21 CST

The angle already is defined as A-D-H and an ideal hbond would have angle 0.

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von
Alexandre PERRET
Gesendet: Donnerstag, 5. Dezember 2013 11:32
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: hydrogen bond criteria

 

Hello VMD users,

 

I found something a bit odd using the hbonds plugin. According to the
plugin, the criteria for the formation of a hydrogen bond are the distance
between the donor D and the acceptor A and the angle D-H-A. The cut-off
angle is by default 20 degrees, which means that D and A are too close to
each other. In my opinion, it should be the angle H-D-A with a cut-off angle
of 20 degrees. What do you think ?

 

Thank you in advance,

Alex

  

--
Alexandre Perret
PhD Student
Groupe de Spectrométrie Moléculaire et Atmosphérique - UMR CNRS 7331
Université Reims Champagne-Ardenne
Campus Moulin de la Housse - BP 1039
51687 REIMS FRANCE
alexandre.perret_at_etudiant.univ-reims.fr
Tél : (+33/0) 3 26 91 33 66
Fax: (+33/0) 3 26 91 31 47
 
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