Is there a limit to the size of the ligands I can dock with Glide?
In Suite 2009, ligands must have no more than 300 atoms. For flexible docking and refine and score, ligands must have no more than 50 rotatable bonds, but for rigid docking and score-in-place, there is no limit on the number of rotatable bonds. In Suite 2008 and 2007, the size limits for all docking jobs are 200 atoms and 35 rotatable bonds. These values are also the default values in Suite 2008. In Suite 2007 the defaults are 120 atoms and 20 rotatable bonds. In Suite 2007, if you have a ligand with no more than 200 atoms but more than 35 rotatable bonds (such as a highly flexible molecule like a peptide or polysaccharide), we recommend generating conformations externally, with MacroModel for example, and then running Glide on all those conformation in rigid-docking mode. In rigid-docking mode, you can enter a rotatable bond limit greater than 35, and these ligands will not be skipped during docking. The limit is enforced in Suite 2008 for rigid docking when running the job from Maest
