Article ID: 1564 - Last Modified: February 12, 2014
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, import the PDB file into Maestro and run the Protein Preparation Wizard. We recommend you perform the complete preparation.
Export the prepared ligand to a file, as follows:
- Click and hold on the "Display Only Selected Atoms" toolbar button and choose Molecule.
- Pick an atom in the ligand.
- Click the Export button to open the Export dialog box.
- Select Workspace for the structure source.
- Select the option "Displayed atoms only".
- Export to a Maestro file.
Proceed to the grid generation. When you set up the docking run, you can use the file you exported for the ligand to dock and as the reference ligand in the Core tab, and choose to compute the RMSD, which is added as a property to the output pose file and added to the Project Table when the results are incorporated.
If you want to compare the docked pose with the structure exactly as it is in the crystal structure, you can extract the ligand at an earlier stage of protein preparation, but in any case it should be after any generation of charge states, as this is important for the RMSD matching process. 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.
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