 the two ligands using</p>
<pre>python $PROTOMSHOME/tools/merge_templates.py -f lig1.tem lig3.tem -o li1-li3.tem</pre>
<p>creating li1-li3.tem.</p>
<p>For single-topology, we need to create template files for the electrostatic and van der Waals perturbation. This is done by</p>
<pre>python $PROTOMSHOME/tools/make_single.py -t0 lig3.tem -t1 lig1.tem -p0 lig3.pdb -p1 lig1.pdb -o li3tli1</pre>
<p>Just as when using <code>protoms.py</code> you will be prompted to type in the corresponding atoms in the two molec