I'd like to retain the first 1000 poses with lowest energy for a ligand when I do docking in Glide. Although I specified "write out at most 1000 poses per ligand", the real output only gave me 2 ligand poses. How do I get more poses?

The "Write out at most [n] poses per ligand" really just sets a maximum number of poses returned. Glide has been designed to generated good poses, not an arbitrary number of poses, regardless of quality. So you may get fewer poses than requested. This is particularly true for Glide XP, for which poses are retained only within a limited Emodel window.

To get more poses, you could try the following:

• Increasing the docking funnel width (i.e., the number of intermediate poses) by adjusting the energy window and poses kept under "Advanced Settings" on the Settings tab.
• Increasing the CvdW cutoff under 'Advanced Settings" on the Output tab, to allow higher-energy results.
• Using SP rather than XP.
• Reducing the clustering criteria under "Advanced Settings" on the Output tab, which will allow more similar results. Depending on your purpose in keeping many poses, this may or may not be helpful.
• Turning off post-docking minimization (on the Output tab), in case the minimizer is discarding higher-energy poses or causing multiple solutions to converge.

Keywords: Glide, more poses

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