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Article ID: 1448 - Last Modified: April 20, 2011

Can I calculate total binding free energies with the Total Free Energy by FEP panel in Desmond?

Additional development is needed to appropriately support the calculation of total binding free energies, which you would run from the Total Free Energy by FEP panel by selecting In complex in the Plan Calculation tab. As a result, absolute binding free energy calculations cannot be properly performed and we recommend that you do not run such calculations until this situation is resolved. Many binding free energy problems can be addressed by calculating the relative binding free energies for one or more ligands, which are supported by the Ligand Functional Group Mutation by FEP or the Ring Atom Mutation by FEP panels. Such calculations usually require significantly less CPU time than a full binding free energy calculation.

Note that absolute solvation free energies are properly supported; you can run these calculations by selecting In pure solvent in the Plan Calculation tab of the Total Free Energy by FEP panel.

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