mat. It is a good idea to check these files to see if the script has defined the molecule properly. 
<p></p>
<li>The steps above now need to be repeated for ligand 3.
<p>
</p>
<li>Now we should have all the force field files for the two ligands. The next step is to solvate them. Start by concatenating the two PDB files
<pre>
cat lig1.pdb lig3.pdb > temp.pdb
</pre>
and then we will create a water box of TIP4P water molecules around this pdb file. Type
<pre>
python $PROTOMSHOME/tools/solvate.py -b $PROTOMSHOM