I have a situation where I want to dock a set of molecules that are atropisomers. The problem I have is that Glide doesn't recognize this and treats the bond as rotatable. What do I do?

The conformation generator in Glide does not consider rotational barriers. However, as of Suite 2010 you can apply torsional constraints so that the rotations about such bonds are restricted. You can set up these constraints in the Torsional Constraints tab of the Ligand Docking panel.

Keywords: Docking, atropisomeric ligands, rotatable bond, Glide, Maestro

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