> Dear Amber user,
> I have done QM/MM md simulations for 20 ligand-enzyme-complexes in a waterbox (Amber10). The enzyme has a zinc in the active site, where the ligand is coordinated.
> I generate a average structures after md .
> What is the best way to calculate the interaction energy for these complexes? I like to compare the energies with experimental Ki values.
> I could'nt use MM-GBSA or PBSA due to zinc in the active site.
> Should I minimize the average structure with QM without water or should I generate a new waterbox around the complex?
> Is it possible to calculate a single QM/MM interaction energy for this type of complex in Amber ( this was done in the paper, from which I have the workflow, but they worked with the Tripos forcefield)?
>
> I hope, anybody has a idea for this problem.
>
> Thanks, Susanne
>
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Received on Thu Mar 10 2011 - 01:00:02 PST
