From: Ahmet Bakan (abakan_at_KU.EDU.TR)
Date: Wed Sep 15 2004 - 07:44:29 CDT

Hi Justin,

I have had written this script about eight months ago before I was aware
that of VMD.
The script involves CHARMm LJ 6-12 parameters and Electrostatic energies for
hbonds that satisfy CutOff Dist and Angle.


-----Original Message-----
From: Justin Gullingsrud []
Sent: Wednesday, September 15, 2004 3:31 PM
To: Ahmet Bakan
Cc: Uday K. Chippada;
Subject: Re: vmd-l: Counting number of hydrogen bonds in the representation

Hi Ahmet,

Interesting script! Do you happen to have a reference for how you
calculate your hbond energies? Also, were you aware that there is a
"measure hbonds" function in VMD that can be used to find hbond
partners that satisfy geometric constraints? See for


On Wed, 15 Sep 2004 11:39:56 +0300, Ahmet Bakan <> wrote:
> Hi Uday,
> Plese find the attached TCL script which calculates hbonding interaction
> energies. You can derive number of hydrogen bonds. The script takes
> 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: [] On Behalf
> Uday K. Chippada
> Sent: Wednesday, September 15, 2004 12:38 AM
> To:
> 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
> and I want to calculate the total number of hydrogen bonds (for a
> 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
> bonds or at least count them.
> Any help would be greatly appreciated.
> Thank you.
> Uday Chippada.

The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"