Hi
I am calculated the decomposition energy of a ligand, which gives for example the following LYS energies (LIGAND)
LIGAND TOTAL Non-Polar Solv. Polar Solvation Electrostatic van der Waals
L GLU 2 -0.83 -0.24 324.47 -324.93 -0.13
L LYS 9 1.35 -0.05 -327.77 330.10 -0.94
L LEU 7 -3.72 -0.46 2.29 -1.90 -3.65
I have a couple of questions:
1) I don’t really understand why the electrostatics and polar solvation energies in teh case of LYS and GLU almost neutralize each other, so that the contribution of a charge residue is almost non-existent, why is so?? They do form hydrogen bonds with water or the other receptor residues.
2) Looking at the total ligand decomposition the total dg on a different case comes almost exclusively from the vDWaals term, is that normal?
LIGAND TOTAL Non-Polar Solv. Polar Solvation Electrostatic van der Waals
ALL LIG RES -38.55 -5.66 46.27 -40.95 -38.21
The total energies look good.
Thanks a lot in advance,
Fabian
Dr. Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
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Received on Thu Nov 19 2015 - 09:00:03 PST
