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.
