Dear Amber community members and Ross,
Thanks for that suggestion earlier.
The difference between gb and pb free energy results is large (-42.0688 and
-25.3752).
*Is this result sufficiently rigorous for a publication purpose or
should I calculate the entropy factor as well using the tutorial*
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section5.htm
Actually I have a series of ligands (some with similar structure and
some from other series) for my target for which I want to compare
binding free energies, docking results and known IC50 values. Which of the
above approach would be better?
Your comments and suggestions will be valuable for my work as earlier.
Waiting for the same...
Thanks once again.
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Tue Jun 08 2010 - 03:30:04 PDT
