[gmx-users] lie calculations

Vytautas Rakeviius vytautas1987 at yahoo.com
Thu Sep 13 09:10:06 CEST 2018

 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 <graham.jackson at uct.ac.za> 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?


Professor Graham E Jackson
Department of Chemistry
University of Cape Town
South Africa
+27 21 650 2531

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