Hello everyone I want to simulate a protein ligand docked complex using GROMOS96 43a1 force field. I have prepared the ligand topology using ATB server. However, I want to know how can I validate the results of ATB when no experimental or computational data is available for small molecule. I have read in Justin's paper that we can calculate octanol-water partition coefficient in biphasic system and correlate the logP and other paramteres with available data. However, in the absence of any experimental or theoretical proof, is there any way by which I can validate the ATB parameters? The small molecule contains groups fllowing groups: N=N, OCH3, Phenyl rings, Cyclohexyl group, -CN, Vinyl group.
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