Article ID: 934 - Last Modified: May 25, 2011
I am running a Glide XP job with default settings, but it is running very slowly. What might be causing this problem?
Glide XP docking should normally take roughly 5 minutes or so per ligand. If you are screening large numbers of compounds, you should consider using SP docking first, then processing the best poses from SP docking with XP docking.
If you have included flexible hydroxyls in the grid generation, then the job will run slower than with a grid that doesn't have flexible hydroxyls. This is because the ligand is being docked to multiple receptor conformations, and naturally the time taken must be greater. However, the time taken scales roughly linearly with the number of hydroxyls, whereas if you generated a grid for each hydroxyl orientation, the time taken would scale exponentially with the number of hydroxyls. So the linear scaling shows a significant efficiency.
Flexible hydroxyls should only be included when hydroxyl motion is important for ligand binding. If you do want to use flexible hydroxyls, you should choose them carefully, to include only those hydroxyls that are important for docking. Including hydroxyls that are not important can waste a lot of resources. To reduce the number of hydroxyls, you should be able to manually pick them in the grid generation stage. We suggest choosing only hydroxyls that are not already making intramolecular hydrogen bonds within the receptor. There is a very low probability that an intramolecular hydrogen bond will be broken with the receptor in order to make a new interaction with the ligand.
Keywords: Glide, flexible hydroxyls, XP docking, speed
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