After doing the restrained minimization (impref) in the Protein Preparation Wizard, the metal ion often moves quite a lot from its original positions. What should I do to keep it restrained?

When you click Preprocess, several dashed lines are created between the protein atoms and the ions. These are zero order bonds which have fixed angle and length. Make sure that all zero order bonds are assigned before you do the minimization, by clicking on Preprocess.

Keywords: Protein prep, metal ions, Maestro

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