With the van der Waals scaling factor in Glide grid generation, do I have an option to customize the vdW scaling of certain residues in the active site rather than scaling all the non polar atoms in the protein?

Beginning with Suite 2009 (Maestro 9.0, Glide 5.5), the receptor vdW scaling can be fully customized. That is, instead of using overall scaling and charge cutoff factors, you can set custom parameters for various receptor residue or atom sets. This is a new section of the Receptor tab in the Grid Generation panel. See the online help or the Glide User Manual for more information.

Keywords: receptor vdW scaling, parameters, grid generation panel, Glide, Maestro

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