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Article ID: 356 - Last Modified: August 13, 2014

Is it possible to assign bond orders to PDB ligands from the command line?

Yes, with the following command:

$SCHRODINGER/run -FROM maestro fix_bond_orders.py input-file output-file

where the input and output files can be in Maestro, PDB, or SD format. This command assigns bond orders (single, double, triple, or zero-order) in the same way as selecting "Assign bond orders" in the Protein Preparation Wizard panel in Maestro, including zero-order bonds to metals.

Keywords: ligand preparation

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