Step 6. LINK_BONDS

When there are covalent bonds that cross the QM/MM boundary, the LINK_BONDS subkey block is required. Since one only defines the 'real system in both the ATOMS key block and the MM_CONNECTION_TABLE subkey block, this key block defines both the initial position of the capping atom and what kind of ADF fragment atom will be used as a capping atom. In this example we have two link bonds, both of which will be 'capped' with capping hydrogen atoms as shown in Figure 5-1b. Below is the LINK_BONDS subkey block for our example.

 LINK_BONDS
   1 - 5 1.380 H
   1 - 2 1.375 H
 SUBEND

The first part of the input specifies the atoms involved in link bonds. Here QM atom 1 forms link bonds with atoms 5 and 2. The column in the input is the link bond a parameter, which is defined as the ratio between the capping bond length in the QM model system and the bond length of the corresponding link bond in the real system. This ratio can be determined by taking the necessary bond lengths from a pure QM calculation of the model QM system, and the bond length from the whole complex. If those are not available, they can be taken from tabulated bond lengths or bond lengths of similar bonds in other complexes. There is an independent a parameter for each link bond. It is VERY IMPORTANT to emphasize that the total energy of the QM/M system is dependent upon the a parameters. Thus, if one is comparing the energetics of two conformational isomers calculated with the QM/MM method, this comparison is only valid if the a parameters used are the same. In our example, ratios of 1.38 and 1.375 were used. This is somewhat typical ratio of C-H to C-C bond lengths, in aliphatic hydrocarbons. The last column in the LINK_BONDS input refers to the ADF fragment for which will be used for the capping atom in the electronic structure calculation. Please, note this fragment must be present in the FRAGMENTS key block of the ADF input.