tion</li>
	<li><code>lig3_box.pdb</code> = the box of water solvating ligand 3, this box will not be used</li>
	<li><code>water.pdb</code> = the cap of water solvating the protein-ligand system in the bound leg simulation</li>
	<p>
For the dual-topology simulations the following files are created:	</p>
	<li><code>li1-li3.tem</code> = the combined template file for the two ligands, used only in this simulation</li>
	<li><code>run_bnd.cmd</code> = the ProtoMS command file for the bound-leg simulation</li>
	<l