Is it possible to fix atoms, so they don't move during an energy minimization?
With MM2, yes. Highlight the atoms that you want to move, then in the MM2 dialog box, General tab, click on the Move Only Selected Atoms option. You could also highlight the atoms you want fixed, then go to the Edit menu and choose Select Atoms -> Select Reverse option. This will highlight the atoms you want to move, which might be easier depending on how many atoms you have and how many you want fixed.