code> - the structure of the first ligand molecule in PDB format</li>
	<li><code>lig3.pdb</code> - the structure of the second ligand molecule in PDB format</li>
	<li><code>protein.pdb</code> - the structure of the COX2 protein in PDB format</li>
</ul>
Both the ligands and protein need to be prepared before they are used with ProtoMS. For instance, you must make sure that they are correctly protonated. You can read more about setting up structures <a href="../prep_struct.html">here</a>.
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