waters from the scoop to the droplet. Therefore, we need to remove them from the scoop PDB-file.<p> 
<pre>sed -i -e "/T4P/d" -e "/TER/d" protein_scoop.pdb</pre>
<p>
Now we have all the files need to run the simulation. As you noticed, this step-by-step procedure create a few files that <code>protoms.py</code> does not generate.
<h5>Making ProtoMS input files</h5>
To make the dual-topology input files for ProtoMS type
<pre>
python $PROTOMSHOME/tools/generate_input.py -s dualtopology -p protein_scoop.pdb -l l