Typically, a QM/MM calculation will involve optimization of the geometry of both the QM and the MM system. To get this, you need to set up the rest of your calculation as a Geometry Optimization:
Go to the Main options panel Select the "Geometry Optimization" template
You can set some more detailed options about the QM/MM calculation:
Go to the QMMM (protein) panel
The values shown in this panel will normally not need to be changed.
