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Article ID: 637 - Last Modified:

I am trying to calculate the RMSD between the docked pose of a ligand, and the same co-crystallized ligand. Unfortunately the atom numbers don't match, resulting in an error. Do I have to renumber the atom numbers or is there any other way of doing it?

Yes, you can use the script,, which is available in your software installation. This script computes the RMSD after automatically renumbering the atoms. It is a command-line script, which you can run as follows:

$SCHRODINGER/run file1 file2

where file1 and file2 are the Maestro files that contain the co-crystallized ligand and the pose file. If you have generated ionization or tautomeric states of your ligand, you should use the -use_neutral_scaffold option to ensure that the multiple bonds patterns and ionization states are ignored when calculating the RMSD.

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