Glide docking produces poses with only chair conformations of cyclohexane rings. How can I get poses with cyclohexyl boat conformations?

By default, Glide generates ring conformations with a narrow energy window (2.5 kcal/mol), deliberately excluding cyclohexyl boat conformations. You can increase the energy window by clicking Advanced Settings on the Settings tab of the Ligand Docking panel, and changing the value in the dialog box that opens.

Alternatively, you could turn off ring sampling entirely (on the Settings tab), so Glide will retain whatever ring conformation is in the input ligand structure.

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