When docking a native ligand with Glide, how do I calculate the RMSD between the docked ligand and the ligand in the crystal structure?

First, extract the ligand from the crystal structure. You can do this in Maestro after importing the PDB file after running the Preprocess step in the Protein Preparation Wizard. Click and hold on the "Display Only Selected Atoms" toolbar button and choose Molecule, then pick an atom in the ligand. Click the Export button, select Workspace for the structure source, select the option "Displayed atoms only", and export to a Maestro file.

Continue with the protein preparation and grid generation. When you set up the docking run, use the file you exported for the ligand, and in the Output tab, select "Compute RMSD to input ligand geometries". The RMSD is added as a property to the output pose file, "glide rmsd to input", which is displayed in the Project Table when the results are incorporated.

If you want to compare the docked pose with the structure as it is in the prepared protein, extract the ligand at the end of the protein preparation instead. The results should not be significantly different.

You can also use the Script Center script rmsd.py to calculate the RMSD, as follows:

$SCHRODINGER/run rmsd.py -use_neutral_scaffold ligand-file pose-file

where ligand-file is the file that you exported, and pose-file is the pose viewer file from Glide docking. The RMSD is printed to standard output. You can write the docked ligand poses to a Maestro file with the RMSD as a property by using -o output-file.

Keywords: Maestro

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