Using Glide XP, I generated 100 output poses for a ligand, but I found that there were many duplicate poses, violating the default RMS deviation and maximum atomic displacement settings. What could have caused this?

When keeping 10 or more poses per ligand there are two situations that could occur.

First, due to the computational cost of accounting for symmetries (e.g., 180 degree rotation of a phenyl), symmetries are not taken into consideration when computing the RMSDs when there are 10 or more poses. This process has been optimized for Glide 5.8 (Suite 2012), and the default is now 100 or more poses, and can be set with the NMAXRMSSYM keyword in the Glide input file.

Second, in earlier releases, if you requested more poses than Glide found distinct poses, Glide supplemented the output with some duplicates (according to the RMSD/dist cutoffs). This behavior has been eliminated in Glide 5.5 (Suite 2009), and only the distinct poses are returned, even if this is less than the number requested.

Keywords: default settings, poses per ligand, RMSD, symmetries, Glide, Maestro

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