tools/ambertools.py -f fragment.pdb -n XDK</pre>
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and this will execute the AmberTools programs <code>antechamber</code> and <code>parmchk</code>, creating the files <code>fragment.prepi</code> and <code>fragment.frcmod</code>, respectively. 
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<li>These files are in Amber format and in order to use them in ProtoMS we need to reformat them into a ProtoMS template file. This file will also contain a z-matrix that describes how the ligand will be sampled during the simulation. To do this, you can type
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