ules. This tool will create <code>li3-li1_ele.tem</code>, <code>li3-li1_vdw.tem</code>, <code>li3-li1_comb.tem</code>, and <code>li3-li1_cmap.dat</code> </p>
<p>Now we have all the files to run the free leg of the simulation. The input file for ProtoMS will be created when we have prepared the bound leg. </p>
<h5>Setting up the bound leg</h5>
<li>First, we will change the name of atom and residue names in the protein PDB file such that they agree with the ProtoMS naming convention. Type
<p> 
<pre>python $PR