contains a directive, telling ProtoMS the name of the solute. The line should read <code>HEADER LI1</code> and can be added by typing
<pre>
sed -i "1iHEADER LI1" lig1.pdb
</pre>
<li>Thereafter, we will create the force field for the ligand using AmberTools. The force field will be GAFF with AM1-BCC charges. Type
<pre>python $PROTOMSHOME/tools/ambertools.py -f lig1.pdb -n LI1</pre>
and this will execute the AmberTools programs <code>antechamber</code> and <code>parmchck</code>, creating the files <code>lig1.