How do I assign proper partial charges to my structures for Glide docking or other applications?

The OPLS_2005 force field used by Glide, MacroModel, Prime, and othe products assigns partial charges automatically at runtime. The partial charge values that can be viewed as labels in Maestro are ignored by default. However, some programs include options to use charges from the input file rather that those that would be assigned by the force field. For example, the Glide Receptor Grid Generation and Ligand Docking panels include a "Use input partial charges" option that applies to the receptor and ligand structures, respectively.

We recommend using the default OPLS_2005-assigned charges, unless you find they are inadequate in some way (please let us know), or you have alternative high-quality charges (e.g., from QM) that you wish to use instead. If you run Glide or other programs using partial charges from the input structure file, you must make sure that all atoms of your structures have valid partial charge properties. OPLS_2005 charges can be assigned to a structure via Tools → Assign Partial Charges in Maestro, or by running any OPLS_2005 calculation (e.g., LigPrep, Impact, MacroModel, or the minimization stage of the Protein Preparation Wizard).

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