Dear all,
I was asked to calculate binding free energy for two polymers, they are both small molecule, the MW are less than 2000. The solvent is water, I have run about 300ns with pemed.cuda. The two polymers sometimes got close to interact with hydrogen bonding and VdW and Elec interaction. My advisor asked me to find a proper way to calculate the binding free energy. But she thought TI, MM-PBSA, FEP were not accurate enough for the simulation, and my simulation was not the same with that of a ligand and a protein. I have no idea what the proper method is, could someone give me some suggestions?
Thanks,
Xiaoquan
2014-01-02
X Sun
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Received on Thu Jan 02 2014 - 11:30:03 PST
