Knowledge Base

Article ID: 356 - Last Modified:

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

Yes, with the following command:

$SCHRODINGER/run 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

Back to Search Results

Was this information helpful?

What can we do to improve this information?

To ask a question or get help, please submit a support ticket or email us at
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles