Can I dock a covalently bound ligand with Glide?
Glide does not perform docking of covalently bound ligands. It requires that the ligand be a single, isolated molecule, so you must break any bonds to the receptor. Starting with Suite 2009, you can perform covalent docking with Prime. Alternatively, you can use MacroModel to perform a conformational search on the covalently bound ligand, using substructures to limit the search to the ligand only. With this approach, ranking a series of covalently-bound ligands could be done using energy differences.
