>
<pre>python $PROTOMSHOME/tools/build_template.py -p fragment.prepi -f fragment.frcmod -o fragment.tem -n XDK</pre>
<p>
this will creates the files <code>fragment.tem</code> containing the ProtoMS template file and <code>fragment.zmat</code>. It is a good idea to check this files to see if the script has defined the molecule properly.
<p> 
<li>Now we have setup the fragment, but there is another "ligand" that we have not mentioned: the water molecules used for the JAWS calculation. These are considered by 