VMD-L Mailing List

From: hirdesh kumar (hirdeshs8_at_gmail.com)
Date: Fri Aug 27 2010 - 23:25:21 CDT

Thanks Axel,
It suggests that I should proceed further with the default 20 degree angle
given in VMD.

On Fri, Aug 27, 2010 at 8:11 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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, **
>