VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Tue Aug 29 2000 - 14:18:45 CDT

Hi,

Unfortunately it is not currently possible to do any of the things you
describe within VMD. Of course, with Tcl scripting, anything is possible ;-).
It should be possible to work with the atom coordinates in Tcl and calculate
distances, angles, etc. But it would be rather painful and likely very
slow. My suggestion would be to simply generate the hbonds you want, then
use the picking tools to figure out which atoms are actually involved in
hbonds. I know that's tedious, but h-bonds simply don't exist as a data
structure in VMD, they're just drawn in.

As far as periodic boxes go, VMD doesn't really have a concept of boundary
conditions or symmetry operations, so no dice there, either.

Regards,

Justin

 
>
> Hi,
> I have used the hbond option in the graphics form to display hydrogen
> bonds and like the ability to change bond distance and angle. It took me
> a few moments to realize that the distance restraint is based on the
> oxygen-oxygen distance though. My question(s)
>
>
> Is there a way to get a listing of all the hbonds that were found?
>
> And, is it possible to calculate and count hbonds that are formed on the
> edges of a periodic box?
>
> Brian Bennion
>
>
>
>
>
> Graduate Research Assistant
> Dep. Medicinal Chemistry, University of Washington
> Tel# (206)616-2779
> BOX 357610 Seattle WA 98195
>
> email--bbennion_at_u.washington.edu
> web page--http://students.washington.edu/bbennion
>
> 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D