VMD-L Mailing List
From: Ana Celia Vila Verde (acavilaverde_at_gmail.com)
Date: Tue Jul 15 2014 - 06:56:42 CDT
If you wanted to find only linear hbonds, then you would make angle=0.
The text below is unclear, I agree: when one mentions an angle D-H-A,
one typically refers to the angle with vertex at H; for a linear HB,
that angle is 180deg. The text in the VMD manual that explains the
"measure hbonds" command is clearer: "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. "
On 15/07/14 11:51, Mary Varughese wrote:
> in vmd hbonds is given as
> 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.
> the default value of angle is given as 20 degrees.
> is this 180-angle =20 as in amber
> for a linear hbond what will be the angle value in vmd; 180 or 0 degree?
> thanking you
> mary varughese