Example A: Cytocine
This is a straightforward example, where the input necessary to perform a QM/MM simulation of cytosine (Figure 5-1) will be constructed.
Step 1. Partitioning the System and the Model QM systemStep 2. Labeling of Atoms (QM, MM or LI)
Step 3. Renumbering of Atoms
Step 4. ADF QM/MM input: Atomic coordinates
Step 5. Connection Table and MM force field types
Step 6. LINK_BONDS
Step 7. Assignment of Atomic Charges
Step 8. Remainder of the QMMM key block
Step 9. Putting it all together: The whole ADF QM/MM input
