Step 3. Renumbering of Atoms

There is a strict rule concerning the ordering of the atoms, based on the QM, MM, or LI atom type designation. All QM and LI atoms must come before any MM atoms. A valid atom numbering for the example system is shown in figure 5-2b. Here the atoms labeled 'QM' or 'LI' in Figure 5-2a are the first five atoms of the molecular system.