pdb -o water_clr.pdb</pre>
<p>Feel free to check the difference between <code>water.pdb</code> and <code>water_clr.pdb</code>, there may be a few less waters in the later, but there might be no difference at all.
Now we have all the files need to run the simulation. As you noticed, there is some difference in the files produced with this step-by-step procedure and those created with <code>protoms.py</code>.
<h5>Making ProtoMS input files</h5>
To make the input files for ProtoMS type
<p>
<pre>python $PROTOMS