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Article ID: 585 - Last Modified: June 7, 2011

I specified 3 poses per ligand for DOCK_POSES_PER_LIGAND, but my "lib" file (with all the docked ligands) only has one structure per ligand (15 in total). Is there something else I need to do to get 3 poses saved per ligand?

This setting does not guarantee that Glide will return 3 poses per ligand; you're just setting an upper bound on the number returned per ligand. For Glide XP in particular you will often get fewer poses than requested, because Glide is searching for good, distinct poses, not an arbitrary number of poses. It might just be a coincidence that Glide found just a single good pose for all 15 of your ligands. Try running with SP, which generally produces more poses than XP.

Also, keep in mind when saving multiple poses per ligand that Glide ranks different poses of the same ligand by Emodel, while it ranks chemically-distinct ligands against one another by GlideScore. So if you have three poses of a given ligand, the 'best' one (from Glide's perspective) is the one with the best Emodel score, not the best GlideScore.

Keywords: dock_poses_per_ligand, Glide XP, saving mutiple poses

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