From: Uday K. Chippada (
Date: Wed Sep 15 2004 - 13:21:59 CDT

Hi Ahmet,

That was an impressive script. But I was not able to get any output files upon running it. It didnt ask me for any parameters (sufix, cut off and angle) as you have mentioned. May be I was doing it wrong?!? Can you tell me where I need to input these parameters?

Also just to let you know, I am using a 3 chain protein (1QSU from protein data bank), surrounded by a water sphere, and I just want to count the number of hydrogen bonds between the chains (excluding water) for all the frames in the simulation (run using NAMD). Please let me know if the script you sent can be used for my case.

Thank you
Uday Chippada.

-----Original Message-----

> Date: Wed Sep 15 04:39:56 EDT 2004
> From: "Ahmet Bakan" <>
> Subject: RE: vmd-l: Counting number of hydrogen bonds in the representation
> To: "'Uday K. Chippada'" <>,
> 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: [] On Behalf Of
> 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 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.