Can I use poses generated with Glide SP or HTVS as input to XP docking?
The conformation generator in Glide (both SP and XP) does exhibit some dependence on the initial conformation, and we have observed better results when starting from relaxed ligand conformations. Since Glide can produce poses with internal ligand strain, we recommend either relaxing these structures prior to running XP (such as with the premin utility) or using the original input ligand conformations for the SP or HTVS docking run for XP docking. Our Virtual Screening Workflow (VSW) actually uses this latter approach.
