Step 5. Connection Table and MM force field types

In order to construct a molecular mechanics potential, the program needs to know the connectivity of the molecular system and the molecular mechanics force field atom-type designations. In this example we are using the AMBER95 force field of Kollman and coworkers [4]. The appropriate AMBER95 atom-types for this molecule are shown in Figure 5-2c. No new atom types need to be introduced to the standard AMBER95 force field to treat this system. However, if this were needed, then the force field file would have to be modified.

Next a connection table needs to be constructed. For this program this needs to be done on an atom by atom basis. Either a fully redundant connection table or a fully non-redundant connection table is acceptable. A redundant connection table refers to one in which the covalent bonds are defined for all atoms. For example, if X is bonded to Y, in the connections for atom X, a bond is defined to atom Y. For the connections to atom Y, a bond is also defined to atom X even though the bond has already been defined. In a non-redundant connection table, when a bond is defined in the connections for atom X, it is not again defined in the connections for atom Y.

We now can begin to construct part of the input, namely the MM_CONNECTION_TABLE subkey block of the QMMM key block. For this example, the MM_CONNECTION_TABLE key block is given below.

MM_CONNECTION_TABLE
 1 CT QM 2 3 4 5
 2 CT LI 1 20 23 24
 3 HC QM 1 
 4 HC QM 1
 5 CT LI 1 17 21 22
 6 N2 MM 7 13 14
 7 CA MM 6 8 11
 8 CM MM 7 9 15
 9 CM MM 8 10 16
10 N* MM 9 12 17
11 NC MM 7 12 
12 C MM 10 11 18
13 H MM 6
14 H MM 6
15 HA MM 8
16 H4 MM 9
17 CT MM 5 10 19 20
18 O MM 12 
19 H2 MM 17
20 OS MM 2 17
21 HC MM 5 
22 HC MM 5
23 H1 MM 2
24 H1 MM 2
SUBEND

The first column is simply the atom number. The atoms defined here MUST be in the same order as defined in the ATOMS key block provided in the previous section. Again, we do not include the capping atoms. The second column shows the AMBER95 atom-types for our system, displayed in Figure 5-2c. The third column is the MM, QM or LI designation. Notice that the QM and LI atoms appear before any MM atoms. The remaining columns are reserved for the connection table. In the above example, a fully redundant connection table is provided.