[gmx-users] LIE interaction energy calculations
feenstra at chem.vu.nl
Wed May 14 11:34:01 CEST 2003
Bert de Groot wrote:
> How large is the ligand? Did you consider FEP calculations? (ie
> gradually letting the ligand (dis)appear in the pocket -- if you do
> the same in water then the difference between the obtained free
> energies (protein-water) might yield a valuable alternative estimate
> of the binding free energy).
Yes, FEP would be the next step, I'd quess. I first wanted to try LIE
to see if it would work, the simulations were already done so that's easy.
The ligands are octane, octanoic acid, and lauric acid. United atoms, so
its 8, 9 and 13 atoms respectively.
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