Unless you have multiple events of binding and unbinding you cannot directly calculate the Ki from EM or MD. You can use approximated methods, e.g. LIE and MM/PBSA (with MD) or LIECE (for a static structure). All of these depend on the choice of empirical parameters.
Best regards, Ran. V. Tanchuk wrote: > > Dear Users, > I am working Drug -- Enzyme Complex. Unfortunately, docking > software (AutoDock) was not able to give any resonable results. I have > tried to use Gromacs and got a resonable binding. The best results > were obtained in the case of simple minimization of the crude > AutoDock's results. The question is how to estimate Ki. > There is also another problem. I have the best correlation between > experimental and calculated results only for the total energy in the > case of optimization (it seems that other kids of energy are not > available without molecular dynamics, but total or any other energies > obtained after molecular dynamics do not correlate). > > Thank you in advance for your help. > > Sincerely yours, > V. Tanchuk
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