Step 2. Set up the QM/MM model system

To define the QM/MM model system you need to:

The different amber types correspond to differently protonated version of the residues. For most residues only one amber type is available, but for some there are more. These are indicated in the list of residues using a color: the pink color means that multiple options are available, and that you have not selected anything. A green color means that you have already selected what amber type to use.

You can change the amber type of a residue by selecting the residue, and next choosing the proper type from the pull-down menu (just below the list of residues).

Select the LYS residue (number 4)
Rotate the image so that you have a good view of the residue
Use the pull-down menu to switch between the neutral and the protonated versions
  (you can see the difference in the picture)

You can make similar changed to other residues if you wish.

At first everything is in the MM region. You can select the residues of your choice, and put them in the QM or MM region using the pull-down menu. You can also move individual atoms to either the QM or MM part using the check boxes next to the atoms. If you have a range of residues selected, and use the pull-down menu to move them to the QM region, ADFinput will try to make the proper cuts. Thus, the parts of the backbone connecting to the MM region will also be kept in the MM region.

Select  a range of residues (for example, residue 7 through 10)
Move them to the QM region using the pull-down menu

The atoms in the QM region will be visualized using larger spheres.

Often you will want to include a solvent in your QM/MM model. This is easy to do: from the Solvent pull-down menu, select the type of solvent to use. Next, specify if the solvent should be put in a sphere or in a box around your protein. Finally, you need to set the size of the box (or sphere). If the size starts with a '+' sign (as is the default), that distance will be added to the size of the protein, otherwise it will be an absolute size.

Select to use 'Water' as solvent