s</code> and <code>out2_jaws</code>.
<p>
<hr align="center"/>
<p> 
<h3><a name="files">Files created by the setup script</a></h3>
<h5>Files describing the fragment</h5>
<ul>
	<li><code>fragment.prepi </code> = the z-matrix and atom types of the fragment in Amber format</li>
	<li><code>fragment.frcmod </code> =  additional parameters not in GAFF</li>
	<li><code>fragment.zmat</code> = the z-matrix of the fragment used to sample it in the MC simulation</li>
	<li><code>fragment.tem</code> = the complete templat