prepi</code> and <code>lig1.frcmod</code>, respectively.<p></p>
<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
<pre>
python $PROTOMSHOME/tools/build_template.py -p lig1.prepi -f lig1.frcmod -o lig1.tem -n LI1
</pre>
this will create the files lig1.tem containing the ProtoMS template file and lig1.z