ig1.pdb lig3.pdb -t li1-li3.tem -pw water.pdb -lw lig1_box.pdb -o run
</pre>
<p>creating <code>run_bnd.cmd</code> and <code>run_free.cmd</code></p>
and for single-topology input files type
<pre>
python $PROTOMSHOME/tools/generate_input.py -s singletopology -p protein_scoop.pdb -l lig3.pdb -t li3tli1_ele.tem -pw water.pdb -lw lig1_box.pdb -o run_ele --outfolder out_ele
python $PROTOMSHOME/tools/generate_input.py -s singletopology -p protein_scoop.pdb -l lig3.pdb -t li3tli1_vdw.tem -pw water.pdb -lw lig1_box.