Article ID: 756 - Last Modified: May 16, 2011
Even though I have "sample ring conformations" on, I always get only one conformation of the 5-ring, therefore missing the best docked structure. The input ligand was minimized, which caused the ring to flip to the "wrong" conformation. What do I do?
Glide uses the same ring-conformation technology as LigPrep, based on an extensive library of ring templates. So 5-membered rings should be sampled. However, Glide accepts ring conformation within a fairly narrow energy window (2.5 kcal/mol), in order to exclude cyclohexyl boat conformations. If your desired ring conformation is more than 2.5 kcal/mol above the lowest-energy conformation, it is possible to increase the energy window in the Settings - Advanced Settings dialog box, or by adding the RINGCONFCUT keyword to the Glide (simplified) input file.
If you want to retain the input conformation, you can turn off ring sampling altogether (in the Glide Settings tab). However, no constraints are placed on the ring conformations during post-docking minimization, so if this minimization step is flipping the ring, you might have to turn it off.
Keywords: 5-membered rings, ring sampling, minimization, Glide, Maestro
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