To setup this simulation type:
<p>
<pre>python $PROTOMSHOME/protoms.py -s singletopology -l lig3.pdb lig1.pdb -p protein.pdb</pre>
<p>
during the setup you will be prompted to type in the atoms in ligand 1 that correspond to atoms in ligand 3. For <code>C38</code> you should type <code>H38</code> and for the 3 methyl hydrogens <code>H43, H41, H42</code> you can simlply leave the line blank to indicate that they should be perturbed to dummy atoms.
<p>
<p>
As with dual-topology, this sets up simulations for t