="files">Files created by the setup script</a></h3>
<h5>Files describing the ligands</h5>
<ul>
	<li><code>lig1.prepi </code> and <code>lig3.prepi</code> = the z-matrix and atom types of the ligands in Amber format</li>
	<li><code>lig1.frcmod </code> and <code>lig3.frcmod </code> = additional parameters not in GAFF</li>
	<li><code>lig1.zmat</code> and <code>lig3.zmat</code> = the z-matrix of the ligands used to sample them in the MC simulation</li>
	<li><code>lig1.tem</code> and <code>lig3.tem</code> = the c