Article ID: 1609 - Last Modified: October 7, 2011
How do I prepare the ligand in my PDB structure?
The ligand in a PDB structure is automatically prepared when you run the Protein Preparation Wizard (on the Workflows or Tasks menu). The Protein Preparation Wizard fixes the bond orders and formal charges, and can run Epik to prepare ionization and tautomeric states. Usually there is no need to run LigPrep on the ligand once it has been through the Protein Preparation Wizard.
If you extracted the ligand from a PDB structure that you imported into Maestro, you can use Assign Bond Orders (Tools menu) to assign the bond orders, and then use LigPrep to prepare the ligand.
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