Article ID: 640 - Last Modified: May 16, 2011
Do I have to minimize the ligand conformation with third-party tools such as MOPAC or Gaussian before I do a docking run?
Glide requires all-atom, 3D structures with good geometry, so we recommend relaxing or minimizing the ligand structures with a high-quality force field prior to docking. If you are docking the ligand from a prepared complex, the ligand has already been relaxed in the 'Impref minimization' step of the Protein Preparation Wizard.
For other ligands (e.g., from a database), we recommend running LigPrep, which can generate alternative ionization, stereochemical, and tautomer states in addition to preparing 3D structures that are suitable for Glide docking.
Glide does have an option to use atomic partial charges from the input structure file, in case you have done QM preparation that included generation of high-quality atomic charges (which might be superior to those assigned automatically by the OPLS force field).
Keywords: relaxing the ligand, Glide
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