I have a template that has the following structure:

Chain A

Chain B

ligand 1 A

ligand 2 A

ligand 3 B

ligand 4 B

I edit my ali file to place 4 dots at the end of the second chain before the *. This results however, in having all four ligands as part of of the B chain in my model. 

How can I fix that? 

Regards.