e>.
<p>
<li>First we need to make sure that the very first line of the <code>fragment.pdb</code> contains a directive, telling ProtoMS the name of the solute. The line should read <code>HEADER XDK</code>, where <code>xdk</code> is the residue name in the fragment, and can be added by typing
<p>
<pre>sed -i "1iHEADER XDK" fragment.pdb</pre>
<p>
<li>Thereafter, we will create the force field for the fragment using AmberTools. The force field will be GAFF with AM1-BCC charge. Type
<p>
<pre>python $PROTOMSHOME/