coop is written to <code>protein_scoop.pdb</code>
<p>
<h5>Setting up the solvation and jaws-waters</h5>
<li>First we will create a droplet of TIP4P water molecules around both ligand and protein. To this, type:
<p> 
<pre>python $PROTOMSHOME/tools/solvate.py -b $PROTOMSHOME/data/wbox_tip4p.pdb -s fragment.pdb -pr protein_scoop.pdb -o water.pdb -g droplet</pre> 
<p>
this will create a droplet with 30 A radius centred on the fragment molecule. The droplet is written to <code>water.pdb</code>
<p> 
<li> The <cod