[Dock-fans] reg free energy calculation

Trent E. Balius tbalius at aol.com
Fri Mar 22 13:03:02 PDT 2013

Hi Vishwambhar 

Scoring functions in DOCK (many of which approximate the binding free energy) have different levels of accuracy.  

See the following for a discussion of DOCK Score: 


 You might consider using the amber score for your calculation:  


Here is a docking tutorial:

Here is a Amber Score tutorial:

Depending on the accuracy that you need, you may need to use an alternative program such as AMBER. 

I hope this helps,


Trent E. Balius, PhD
Shoichet Lab – Dept. of Pharm Chem,
University of California, San Francisco
           1700 4th Street
           Box 2550
           San Francisco, CA 94158     
Office: Byers Hall, Rm 509
URL: http://docking.org/~tbalius



-----Original Message-----
From: Vishwambhar Bhandare <vishwayogi at gmail.com>
To: dock-fans <dock-fans at docking.org>
Sent: Sat, Mar 9, 2013 6:52 am
Subject: [Dock-fans] reg free energy calculation

Dear all, 

I Have to do free energy calulations using dock6.5 

Is there any tutorial or guide available for doing this???

Thanks and Regards, 
Centre for Bioinformatics 
Pondicherry University

Note: Strictly confidential to Vishwayogi

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