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Article ID: 212 - Last Modified: May 4, 2011

Can I use QM/MM to calculate a protein-ligand binding energy? I would like to treat the ligand quantum mechanically and the receptor with the OPLS forcefield.

The script qsite_binding_energies.py can be used for this calculation. You can download this script from the Script Center. The ligand is minimized in the binding site using QSite, where the ligand is treated quantum mechanically and the receptor is treated with molecular mechanics. The energy of the receptor and the ligand are also each calculated alone, and the binding energy is computed by:

E(bind) = E(complex) - E(receptor) - E(ligand)

The basis set and the level of theory for optimizing the QM regions can be specified using the options -basis amd -dftname respectively. There are other parameters for customizing the calculation as well - to view the list of all options, run on the commandline:

$SCHRODINGER/run qsite_binding_energies.py

Keywords: protein, ligand, binding energy

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