Hi I think you should check this paper:Åqvist J, Medina C, Samuelsson JE. A
new method for predicting binding affinity in computer-aided drug design.
Protein Engineering, Design and Selection. 1994 Mar 1;7(3):385-91.It explains
everything and gives example of use.And yes with different water models you
should expect more or less different results.
Also as you see those fitting coefficients in paper like 0.5 or alpha or beta
etc. I suggest refitting with your own data-set water model force field etc. as
those numbers depend on such things. That became clear far later after this
original paper.
On Wednesday, September 12, 2018, 6:35:23 PM GMT+3, Graham Jackson
wrote:
Hi All
I have looked at the manual and can execute LIE but I want to understand the
process. The manual gives instructions but no background theory. The theory I
have seen does not explain how GROMACS does the calculation. I have a
simulation of a ligand bound to a receptor embedded in a POPC membrane. I also
have a simulation of the ligand in water. I use these two for the lie
calculation. Is this correct and does the choice of water (spc TIP3P Tip4P)
matter?
Thanks
Graham
—
Professor Graham E Jackson
Department of Chemistry
University of Cape Town
South Africa
+27 21 650 2531
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