Why does Glide produce duplicate poses even when a large RMS cutoff to discard duplicates is specified in the Output tab?
If the requested number of poses per ligand is larger than 10, Glide does not take symmetries into account when clustering, due to the computational cost of those calculations for larger sets. As a result, it is possible in these cases to get poses that are duplicates, when atom reordering is considered. The efficiency has been improved in Suite 2012 (Glide 5.8), and the cutoff is now 100 poses by default; the cutoff can be set with the NMAXRMSSYM keyword in the Glide input file.
#24: In my Glide docking results I am seeing multiple very similar poses for a given ligand. I thought Glide was supposed ...
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