Examples for how this tool created the data files in the examples/amoeba directory: ** water_dimer: % python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba % python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo ** water_hexamer: % python tinker2lmp.py -xyz water_hexamer.xyz -amoeba amoeba_water.prm -data data.water_hexamer.amoeba % python tinker2lmp.py -xyz water_hexamer.xyz -hippo hippo_water.prm -data data.water_hexamer.hippo ** water_box: % python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643 % python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643 ** ubiquitin: % python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new