VMD-L Mailing List

From: politr_at_huji.ac.il
Date: Fri May 30 2008 - 10:59:28 CDT

Dear VMD users and developers,
I would like to ask about hydrogen bonds. I saw in VMD manual how to
define hbonds: *measure hbonds /cutoff/ /angle/ /selection1/
[/selection2/]*: Find all hydrogen bonds in the given selection(s),
using simple geometric criteria. Donor and acceptor must be within the
/cutoff/ distance, and the angle formed by the donor, hydrogen, and
acceptor must be less than /angle/ from 180 degrees.
I can't understand the definition of angle. What does it mean "less than
/angle/ from 180 degrees". Let say I need the angle formed by
O-H-----O (teta in the picture attached) to be greater than 120 what
angle should I use in "measure hbonds....." and what selection
definitions. What should I do if I need beta (in picture attached) to be
less than 30.

Thank you in advance
Regina


204107_1-F1.jpg