Article ID: 785 - Last Modified: May 16, 2011
How do I dock ligands that contain metals with Glide?
A ligand must be a single molecule in order to dock it with Glide. However, the OPLS force fields used by Glide for docking do not support covalent bonds to metals; rather the metals must be treated as ions. Therefore, the only way to dock such a ligand is to use zero-order bonds between the metals and the ligating atoms. Be sure to adjust the formal charges of the metals and ligating atoms accordingly. If your structure has single bonds to the metal, you can turn them into zero-order bonds by decreasing the bond orders by one (there is a button on the Build toolbar in Maestro that does this). If they do not, you can draw in the bonds with the Draw tool and then change them to zero-order bonds. The zero-order bonds essentially create constraints on the metal coordination geometry. Note that this means that the input structure must have reasonable coordination geometry already. You might want to turn off the post-docking minimization step of Glide (on the Output tab), because minimization of strained initial poses could result in some distortion of the coordination geometry.
Keywords: metal ligands, zero-order bonds, covalent bonds, Glide
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