From: Ahmet Bakan (abakan_at_ku.edu.tr)
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:
HBONDING 3.2
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.
Cheers,
Ahmet
==========ABC==========
Ahmet Bakan
Chemistry, Junior
Koc University
abakan_at_ku.edu.tr
ICQ #86167698
http://home.ku.edu.tr/~abakan
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] 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/proteologics.com ========== +972 8 9475666 ========== It's not whether you win or lose, it's how you look playing the game. **************************************************************************** ** This e-mail message, together with any attachments, contains information of Proteologics, Ltd (Rehovot, Israel) that may be confidential, proprietary copyrighted and/or legally privileged, and is intended solely for the use of the individual or entity named in this message. If you are not the intended recipient, please notify us immediately and do not disclose, distribute, or retain this e-mail or any part of it. Proteologics, Ltd reserves the right to monitor all e-mail communications through its network. ** eSafe scanned this email for viruses, vandals and malicious content. ** **************************************************************************** **
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