omplete template (force field) file for the ligands in ProtoMS format</li>
</ul>
You can read more about the setup of ligands <a href="../prep_struct.html">here</a>.
<h5>Files describing the protein</h5>
<ul>
	<li><code>protein_scoop.pdb</code> = the truncated protein structure</li>
</ul>
You can read more about the setup of proteins <a href="../prep_struct.html">here</a>.
<p> 
<h5>Simulation specific files</h5>
<ul>
	<li><code>lig1_box.pdb</code> = the box of water solvating ligand 1 in the free leg simula