From: Axel Kohlmeyer (
Date: Sat Nov 11 2006 - 18:57:25 CST

On Sat, 11 Nov 2006, Adelene Sim wrote:


AS> Hi, I'll like to know if it is possible to plot a graph for the number of
AS> hydrogen bonds versus time in a system where a protein is being stretched
AS> (e.g. like the stretching Deca-alanine tutorial). Also, is there a way to
AS> measure the percentage helicity (and also plot a graph) with time?

i am not aware that there is a plugin yet that can do out of the
box what you want. however, all the components are there
(counting hydrogen bonds, plotting functions, assigning/computing
the secondary structure), so it would only take some smart
tcl/vmd scripting to make this work or even turn it into
a directly usable plugin with a GUI frontend. at least for
the hydrogen bond counting between two selection this would
be of general use.


AS> I've been told that these can be done in the Extension menu of VMD, but I
AS> can't seem to find any way to do that, except perhaps plot bond energies,
AS> which isn't really what I want.
AS> Thanks in advance!
AS> Adelene

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.