lation you need to execute
<p>
<pre>$PROTOMSHOME/protoms3 run_jaws.cmd</pre>
<p>
The calculations will take approximately 10 h to complete.
<p>
<h5>Analysis</h5>
When the simulations are finished you need to analyse the simulation and conclude on a location for the waters in the binding site. We should start by separating the global pdb of your simulation into individual snapshots. Go to the directory called <code>out_jaws</code> and run:
<pre>
python $PROTOMSHOME/tools/divide_pdb.py
</pre>
and then, to vis