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Article ID: 918 - Last Modified: May 25, 2011

When preparing a Glide grid, the native ligand is removed. How do I specify the native ligand as the core to be used for RMSD calculations?

First, create an entry for the native ligand. With the (prepared) structure in the Workspace, select the ligand molecule, and create an entry for the selected atoms.

With this reference molecule in the Workspace, use the Core tab of the Ligand Docking panel to set up the RMSD calculation with respect to the desired core atoms of that molecule. If you don't want to apply a docking constraint to the core atoms, select the "Use for RMSD calculations only" option.

The simplest way to get the SMARTS pattern for the reference core is to select the desired atoms, and then click "Get From Selection", to let Maestro generate the SMARTS pattern for you.

Keywords: Glide, grid, core, RMSD

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