From: Peter Freddolino (
Date: Tue Sep 26 2006 - 16:00:11 CDT

> It looks like I finally understood: when you mean "angle D-H-A", you
> mean "angle between the DH and HA vectors, while I mean \hat{DHA}, the
> angle between vectors HD and HA.

I do mean the angle between vectors HD and HA, \hat{DHA}. You might want
to measure this again, because in your original email you said that the
angle you were expecting was 27.98, which is the angle between vectors
HD and DA, and is not related to the quantity of interest (this was
measured in VMD).

The geometric criterion we're using stems from the charmm19 potential
implementation of hydrogen bonds (Brooks et al., J. Comput. Chem. 4:187,
1983), which pays attention to the D-H-A and H-A-AA angles.

> And also, last but not least, would implementation of other criteria be
> acceptable?

The easiest way to do such a thing is probably to write a tcl script to
draw something between hydrogen bonds that meet these criteria. Is there
any particular reason you want to measure this angle differently?