pdb -o run_vdw --outfolder out_vdw
python $PROTOMSHOME/tools/generate_input.py -s singletopology -p protein_scoop.pdb -l lig3.pdb -t li3tli1_comb.tem -pw water.pdb -lw lig1_box.pdb -o run_comb --outfolder out_comb
</pre>
<p>creating <code>run_ele_bnd.cmd</code>, <code>run_ele_free.cmd</code>, <code>run_ele_gas.cmd</code>, <code>run_vdw_bnd.cmd</code>, <code>run_vdw_free.cmd</code>, <code>run_vdw_gas.cmd</code>, <code>run_comb_bnd.cmd</code>, <code>run_comb_free.cmd</code> and <code>run_comb_gas.cmd</code> <