Dear Amber community members,
I have performed MMPBSA analysis on a series of ligands with a given
protein.
Now I want to rationalize various values thus obtained.
One obvious value is the DeltaG binding, the more -ve it is more stronger
the interaction. Also I could make some sense out of the values for VDWAALS
and EEL terms and correlate them to the interactions with various ligands.
But I found that analyzing other values like DeltaGsolv, EPB, EGB, ESUR,
ECAVITY are not so easy to relate directly with properties and interaction
of various ligands. Also deeper explanation associated with these terms is
not given in the tutorial.
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm
I have some vales given in the table below.
It would be really helpful if somebody could point out a paper or
discussion relating to interpretation of these values and how one can
logically connect them to the properties and interactions of a series of
ligands with the protein???
Thank you all.
*Ligand*
*MM-PBSA/GBSA*
*Contributions*
*PB*
*GB*
*ÄGsolv*
*VDWAALS*
*EEL*
*ÄG binding*
*ÄG binding*
*PB*
*GB*
X
-48.11
-18.75
-25.38
-42.07
41.48
24.79
Y
-52.38
-20.56
-25.45
-40.27
47.45
32.67
Z
-75.85
-12.88
-39.83
-56.63
48.89
32.10
--
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 Thu Jan 19 2012 - 05:00:11 PST
