VMD-L Mailing List

From: Ahmet Bakan (abakan_at_KU.EDU.TR)
Date: Wed Sep 15 2004 - 03:39:56 CDT

Hi Uday,

Plese find the attached TCL script which calculates hbonding interaction
energies. You can derive number of hydrogen bonds. The script takes three
inputs:
SufixForOutFile CutOffDistance CutOffAngle
It does not take atom selections as input and assumes that there are two
interacting chains.

Hope this works for you,

Ahmet

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Uday K. Chippada
Sent: Wednesday, September 15, 2004 12:38 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Counting number of hydrogen bonds in the representation

Hi,

I have a simple question on VMD. I am working on a protein and did SMD
simulations on it in NAMD. After the simulation I am visualizing it in VMD,
and I want to calculate the total number of hydrogen bonds (for a particular
distance cut off say 3.0 and a particular angle cut off of say 30) at each
frame. I want to know if there is a method to display the number of hydrogen
bonds or at least count them.

Any help would be greatly appreciated.

Thank you.
Uday Chippada.


  • application/octet-stream attachment: hbond.tcl