VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 27 2010 - 09:41:22 CDT

On Fri, 2010-08-27 at 18:49 +0530, hirdesh kumar wrote:
> Hi All,
> The default angle D-H-A angle is 20 degree in HBond plugin
> (http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/) but in many
> research papers the angle is less than 120 degree. e.g.
> http://peds.oxfordjournals.org/cgi/content/full/16/7/489.
> Now if I change the default angle from 20 degee to 120 degree, the
> system got hang and no result come out.?
> Can anybody suggest me what to do?

those two definitions are incompatible.
the 20 degree angle looks at

_/ H
D------A

where as the 120 degree angle looks at

D--H--A

if D--H would be the same distance as H--A,
then 120 degree would be equivalent to 30 degrees
in the other definition. but that is normally
not the case and the angle would be different.

this is a bit of a religious issue, but in my
personal opinion, the first definition makes
much more sense.

cheers,
    axel.

>
>
> Hirdesh 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.