Dear Gmx Users! I do protein-ligand simulations and I am interested in binding free energy. My ligand is not charged molecule, there is no specific binding so hydrogen bonding and hydrophobic interactions are responisble for binding. I have experimental data from ITC of binding free energy.
I am wondering whether application of Umbrella Sampling would be a good aplication. I would like to put e.g. 10 ligands around my protein (200 residues) and see which of them went into my structure deep (stronger interaction) and then using position restrained dyunamics of my protein and other ligands pull crucial ligand and perform windows for Umbrella Sampling then obtaining free energy? The second thing I would like calculate is binding free energy of the second "layer" of ligands - I mean: they do aggregate one on the another, so in this case will Umbrella Sampling can be used to pull ligand from the another which stacked to my protein (posre of my protein and 1other ligands)? The third thing I am interested is chemical potential of my ligand in this system. Can you please suggest some technique to obtain it - further reading, tutorials? Thank you in advance, Steven
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