i>
	<li><code>jaws1_box.pdb</code> = a visual representation of the dimensions in which your JAWS waters are constrained</li>
	<li><code>water.pdb</code> = the cap of water solvating the protein-ligand system</li>
	<li><code>water_clr.pdb</code> = the cap of water solvating the protein-ligand system, minus any water molecule which was overlapping with the JAWS simulation area</li>
	<li><code>run_jaws.cmd</code> = the ProtoMS input file for the JAWS simulation</li>
</ul>
You can read more about the input fil