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
SufixForOutFile CutOffDistance CutOffAngle
It does not take atom selections as input and assumes that there are two
interacting chains.

Hope this works for you,


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


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