VMD-L Mailing List

From: Salomon Turgman Cohen (sturgman_at_gmail.com)
Date: Thu Apr 25 2013 - 13:13:57 CDT

Hello,

I have the need to detect hydrogen bond like interactions in a system
consisting of amines and some ions. I was thinking the best way to do this
is to use the salt-bridges or h-bonds extension but I cannot quite
understand how to adapt them to my system.

What I would like to do is define a set of donors, hydrogen, and acceptors
according to their types. So I will give the program something like this:

hbonds=((NH3,H3,OO),(NH2,H2,OO),(NH1,H1,OO),...)

In this manner I will tell VMD to look for the those interactions according
to specific distance and angular cutoffs. What would be the best way to
implement something like this? Should I work from the current hbond plugin
and generate my own, or would it be better to write a script from scratch?
Could I use python scripting? Or would I need the TCL functionality in this
case?

Salomon 

-- 
Salomon Turgman Cohen
Postdoctoral Associate
Cornell University
(919) 341-9650