>
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<h3>Simple setup</h3>
<h5>Setup</h5>
The simplest way to set up the simulation is by typing the following
</p>
<p>
<pre>python $PROTOMSHOME/protoms.py -s jaws1 -p protein.pdb -l fragment.pdb </pre>
</p>
this sets up one JAWS stage 1 simulation, to locate the waters which can be placed 2 A around your ligand.<p> The simulations will run 5 m equilibration steps and 40 m production steps. Output will be printed to files every 100 k moves.
<p>
the <code>-s jaws1</code> argument tells the 