 However, you may wish to find the location of waters in any area of your simulation (though normally it will include your binding site).
</p>
<p>
You can define any desired area (in box shape) of your simulation to run JAWS on, by specifying the box origin and dimentions with the flag <code>--gcmcbox</code>, such as it is done below
<p><pre>
python $PROTOMSHOME/protoms.py -l fragment.pdb -p protein.pdb -s jaws1 -c big --gcmcbox 59 31 23 8 8 8
</pre></p>
where the box will be a cube of 8A, with the "lower" 