Step 2. Labeling of Atoms (QM, MM or LI)

Once a partitioning of the system has been established, one needs to designate each of the atoms in the full system as QM, LI or MM atom type. For the example system, these designations are shown in Figure 5-2a, where the atoms that are not labeled are MM atoms.

Figure 5-2 Labeling of the example model. a) QM, MM and LI designations. Atoms not labeled are 'MM' atoms. The dotted polygon encloses the QM region of the model. b) Atom numbering of the entire system. Note that the QM and LI atoms precede any MM atoms. c) The AMBER95 force field atom type designations.

All atoms within the dotted polygon are 'QM' type atoms. The atoms outside of the QM region will either be MM or LI atoms depending on whether they are part of a link bond or not. The covalent bonds that cross the QM/MM boundary are termed the link bonds. In the example system, there are two such covalent bonds. The atoms that lie on the MM side of the link bonds are labeled the LI atoms. Thus, these are all of the atoms that lie outside the dotted polygon that have a covalent bond to QM atoms. If there are no covalent bonds that traverse the QM/MM boundary, then there will be no LI atoms.