From: François-Xavier Coudert (
Date: Tue Sep 26 2006 - 11:18:22 CDT

Hi all,

I have a problem understanding the criterion used for HBonds
representation. From the doc:

     Given an atom D with a hydrogen H bonded to it and an atom
     A with no hydrogen bonded to it, a hydrogen bond exists between
     A and H iff the distance ||D-A|| < dist and the angle D-H-A < ang,
     where ang and dist are user defined.

I assume the angle criterion is H-D-A < ang rather than D-H-A, and I
don't think the "atom A with no hydrogen bonded to it" is enforced,
otherwise no H bond would ever occur in water. Nonetheless, in the
attached xyz file, the DA distance is 2.59 (as labeled by VMD itself)
and the HDA angle is 27.98 (once again measured by VMD). But in Hbonds
representation with distance cutoff 3.5 and angle cutoff 30, no H bond
is displayed (I use VMD 1.8.5).

I supposed there's something I've overlooked, but what?

Thanks for your help,

  • chemical/x-pdb attachment: