E/data/wbox_tip4p.pdb -s temp.pdb -o lig1_box.pdb
</pre>
this will solvate both ligands using standard settings, i.e. it will be 10 A between the solute and the edge of the box. A pre-equilibrated box of TIP4P water molecules located in <code>$PROTOMSHOME/data/</code> is used. The box is written to the file lig1_box.pdb. 
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<li>The next step differ if we want to setup a dual-topology or single-topology simulation. We will start with the dual-topology setup.
<p>We need to combine the template files for