How do I perform docking manually? After I get a pose from Glide, I would like to re-adjust the ligand manually and find out the docked energy for the re-adjusted pose. How can I do this?

You can adjust the structure manually in Maestro with the toolbar buttons. To reposition the ligand as a whole, display the ligand and the receptor in the Workspace, and use the Local Transformation button to move and rotate the ligand (select Molecule from the toolbar button menu and click on the ligand to select the ligand for transformation). With the Adjust button, you can alter specific bond lengths, bond angles, and dihedrals. To ensure that you do not have bad contacts when you adjust the ligand, you can turn on the display of contacts.

Once you have generated a new pose of the ligand, you can run Glide in Refine mode or Score in Place mode. Refine mode minimizes the input ligand pose prior to scoring; the minimization is advisable because you may have introduced clashes while adjusting the pose manually. Score in Place mode just scores the ligand without doing any minimization.

You could also perform a MacroModel Minimization or CSearch on the ligand (freezing the receptor structure) to generate a more reasonable starting pose for Glide.

Keywords: docking manually, toolbar, local transformation, adjust, manual docking, Glide, Maestro

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