Is there a way of using QM-generated partial charges when docking ligands with Glide?

Yes, you can use the QM-Polarized Ligand Docking workflow (QPLD), which uses semiempirical or full QM ESP charges generated by QSite for the ligand. These charges can be calculated either for the free ligand, in water or in the gas phase, or for the ligand in the MM field of the receptor. The workflow first docks the ligands, then generates new charges, and finally redocks the ligands with the new charges.

Keywords: QM, partial charges, Glide, QPLD

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