3>
<ul>
	<li><code>fragment.pdb</code> - the structure of the small fragment molecule in PDB format</li>
	<li><code>protein.pdb</code> - the structure of the N-terminal domain of HSP90 in PDB format</li>
</ul>
Both the fragment and protein have been prepared for use with ProtoMS. For instance, they are correctly protonated. If using your own structures, you must make sure they are prepared correctly prior to simulation. You can read more about setting up structures <a href="../prep_struct.html">here</a>.
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