[gmx-users] ATB parametrization of small molecule

Sun Iba sun.iba2 at gmail.com
Wed Aug 31 10:51:05 CEST 2016

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.

Thank you

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