I successfully built a homology model with Prime, but my ligand does not have the correct bond orders. I want to use this structure as input for another Prime job (e.g., a loop prediction). What should I do?

It's very likely that you will not need to do anything. Before the main Prime job is run, a program is automatically run that will fix the bond orders and formal charges of the ligand, as long as the hydrogens in the structure are correctly placed.

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