Step 7. Assignment of Atomic Charges
Perhaps the most dubious aspect of the QM/MM approach involves the non-bonded electrostatic interaction between the QM and MM regions. The ADF QM/MM extension currently only supports placement of static point charges on MM atoms. At the moment, you have two options. First, you can chose to have the MM point charges to interact with the electron density of the QM model system, thereby allowing the wave function of the QM system to be polarized. Alternatively, you can assign static point charges to the QM atoms which interact with MM point charges as would happen if the whole system were treated with a molecular mechanics force field. In this example, we will choose the latter, using the standard AMBER95 charges cytosine. To specific how the electrostatic interactions between the two regions are treated, one uses the ELSTAT_COUPLING_MODEL keyword in the QMMM key block and sets it equal to 1.
In ADF QM/MM the atomic point charges can be assigned on an atom-type basis, where the point charges are taken from the force field file. It can also be defined on a per atom basis, where a unique charge is assigned to each atom in the molecular system in the CHARGES subkey block. Since the charges in AMBER95 are assigned according to the nucleic or amino acid, we must assign the charges on a per-atom basis. Given below is the CHARGES subkey block with the appropriate AMBER95 point charges assigned to the system. The first column in this subkey block is the atom numbering. It is important to use the right atom number instead because the program actually determines the charges on each atom individually by searching for the atom number within this key block. Charges don't have to be in order.
ELSTAT_COUPLING_MODEL=1 CHARGES 1 0.0000 2 0.0000 3 0.0000 4 0.0000 5 0.0000 6 -0.9530 7 0.8185 8 -0.5215 9 0.0053 10 -0.0484 11 -0.7584 12 0.7538 13 0.4234 14 0.4234 15 0.1928 16 0.1958 17 0.0066 18 -0.6252 19 0.2902 20 -0.2033 21 0.0000 22 0.0000 23 0.0000 24 0.0000 SUBEND
