In my receptor there is a cofactor (Zn) that interacts with 3 different residues of the receptor and also with the ligand. Should I delete the bond between the cofactor (Zn) and the ligand before running Glide?

Yes, you should remove the Zn-ligand zero-order bond prior to running the Glide Grid Generation job. Otherwise, picking the ligand to define the active site will also select the metal and attached receptor atoms, because atoms connected by zero-order bonds are considered by Maestro to be part of the same molecule. (This behavior can be changed in the Preferences panel.)

Keywords: zero-order bond, grid generation , picking the reference ligand, cofactor, Glide

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