Article ID: 658 - Last Modified: May 3, 2011
Is there a script that highlights or lists the most relevant contributions (electrostatics and van der Waals) to the interaction between a ligand (given pose) and the active site residues? I'm interested in the ligand pose results from long MD simulations, followed by energy minimization.
For visualizing Glide results, we recommend generating Glide XP descriptors (requires an XP descriptors license) and viewing the results in Maestro via the XP Visualizer. This tool will show the various components of the XP GlideScore, and it highlights the ligand and receptor atoms involved in the various interactions.
Glide also has a feature for computing per-residue electrostatic, van der Waals, and H-bonding interaction energies. There is an option on the Output tab of the Ligand Docking panel for enabling these calculations. The per-residue energies are strored as structure-level properties in the output pose file, so they can be seen in the Project Table. Also, the pose-viewer mode of the Project Table (Entry → View Poses) can display these energies by coloring the receptor residues according to the per-residue energies with the displayed ligand pose.
There are a couple of scripts on our website (Resources & Downloads → Script Center) that might interest you. The "XP Atom Energies" script breaks down some of the XP descriptor terms into per-atom scores; they are stored as atom-level properties, so you can label atoms with the scores in Maestro. There also is the "Pose Filter" script, which filters a pose file based on desired ligand-receptor interactions.
If you're starting from a non Glide-generated complex you might find the script: "Component Interactions" useful. It is available on our script center in the Molecular Mechanics section. It uses MacroModel to calculate interaction energies.
Keywords: per-residue interactions, XP descriptors, component interactions, XP Atom energies
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