I have extracted a ligand from a PDB structure. How do I prepare the ligand for modeling, by adding multiple bonds, hydrogens, and generating reasonable ionization states?

From Maestro, open the Protein Preparation Wizard, and click Preprocess in the Import and Process tab to add multiple bonds and hydrogens. To generate ionization states, click Generate States in the Review and Modify tab. You must have an Epik license for this task.

If you want to run the preparation from the command line, you can use $SCHRODINGER/utilities/prepwizard. The options for preparing the structure are given in the usage message.

You should always check that your structure is reasonable before proceeding to use it in other applications.

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