RE: Binding free energy of a protein complex

From: Ahmet Bakan (
Date: Mon May 03 2004 - 06:02:29 CDT

Hi Gadi and All,

I have attached a script, which calculates the electrostatic, vdW, and
Hbonding energy of a protein complex within a CutOff distance.
Works like this:
You get
#OfPairsWithinCutOffDistance ElectEnergy vdWEnergy #OfHBonds HbondEnergy
And a file of list of above interactions for all pairs.

Could you tell me your ideas on the script? I would like to develop it to
get a better measure of binding energy.


Ahmet Bakan
Chemistry, Junior
Koc University
ICQ #86167698

-----Original Message-----
From: [] On Behalf
Of Gadi Oron
Sent: Monday, May 03, 2004 10:06 AM
To: NAMD Mailing List
Subject: namd-l: Binding free energy of a protein complex

Dear everyone,

Did anyone had success calculating the binding free energy of a protein
complex using NAMD?

I am looking for someone to lend me hand setting up such a calculation,
and I am willing to pay for the work.

Contact me.

Best regards.

================= Gadi ORON, PhD -o- Proteologics ======================
========== gadi/at/ ========== +972 8 9475666 ==========
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