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Article ID: 1051 - Last Modified:

What can I do if the Prime step in my Induced Fit Docking run fails?

This can happen if the receptor contains unrecognized residues. Before starting the Induced Fit Docking protocol on a given receptor, it is helpful to check that Prime recognizes any modified amino acid residues the receptor contains. Choose Analyze Energy from the Task option menu in the Prime Refinement panel and run the job to check that the starting energy for the complex is reasonable and at the same time detect any unrecognized residues. If unrecognized residues are found, mutate them to residues that are recognized by Prime before beginning the IFD protocol.

Keywords: IFD

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