VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 30 2008 - 15:00:52 CDT

The description of "angle" means that theta - 180 < /angle/, so, for
example, to get theta > 120 you should use 60 for /angle/. The
selections you use are just the entire set of atoms that you want to
search for hydrogen bonds (for example, to get a list of all hydrogen
bonds matching your criteria in a protein, you would use a selection of
protein, and then do [measure hbonds 3.0 60 $sel]). There isn't a simple
way (as far as I know) to access beta; you'd have to approximate based
on trig identities or write your own script.
Best,
Peter

politr_at_huji.ac.il wrote:
> 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
>
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>