diff --git a/pdb2pqr/pdb2pqr/ligand/__init__.py b/pdb2pqr/pdb2pqr/ligand/__init__.py
index 3614edc98..50ae58a92 100644
--- a/pdb2pqr/pdb2pqr/ligand/__init__.py
+++ b/pdb2pqr/pdb2pqr/ligand/__init__.py
@@ -10,19 +10,42 @@ assert sys.version_info >= (3, 5)
 
 
 # TODO - this belongs in a configuration file somewhere other than here.
-# PARSE radii data for C, N, O, S, H, Br, F, P are from Sitkoff et al's paper:
-# 
-#   Sitkoff D, Sharp KA, Honig B. Accurate Calculation of Hydration Free
-#   Energies Using Macroscopic Solvent Models. J Phys Chem 98 (7) 1978-88,
-#   1994. J. Phys. Chem. 1994, 98, 7, 1978–1988
 #
-# See also the AMBER mailing list: http://amber.ch.ic.ac.uk/archive/.
-# 
-# The van der Waals radius is used for chlorine.
-PARSE_RADII = {
-    "C": 1.70, "N": 1.50, "O": 1.40, "S": 1.85, "H": 1.00, "Br":2.50,
-    "F": 1.20, "P": 1.90, "Cl": 1.75}
-
+# When using these tables, the most specific Sybyl atom type should be used
+# first and then the generic element should be used
+RADII = {
+    # NOTE - these are not the original PARSE radii but they are the ones
+    # included in the previous version of PDB2PKA so I'm preserving them for 
+    # posterity. There's a claim they came from
+    # http://amber.ch.ic.ac.uk/archive/ but that link no longer works.
+    "not parse - do not use": {
+        "C": 1.70, "N": 1.50, "O": 1.40, "S": 1.85, "H": 1.00, "Br": 2.50,
+        "F": 1.20, "P": 1.90, "Cl": 1.75},
+    # These are the PARSE radii from Table 4 of
+    # http://doi.org/10.1021/j100058a043
+    "parse": {
+        "C.1": 2.00, "C.2": 2.00, "C.3": 2.00, "C": 1.70, "H": 1.00,
+        "O": 1.40, "N": 1.50, "S": 1.85},
+    # These are the ZAP radii from Table 2 of
+    # http://doi.org/10.1021/jm070549%2B. Bondi radii should be used for
+    # atoms not found in this table.
+    "zap9": {
+        "C": 1.87, "H": 1.10, "O.co2": 1.76, "N": 1.40, "S": 2.15, "F": 2.40,
+        "Cl": 1.82, "I": 2.65},
+    # These are the Bondi radii from Table 2 of
+    # http://doi.org/10.1021/jm070549%2B
+    "bondi-zap": {
+        "C": 1.7, "H": 1.20, "O.co2": 1.52, "N": 1.55, "S": 1.80, "F": 1.47,
+        "Cl": 1.75, "I": 1.98},
+    # These are the Bondi radii from Table I of
+    # http://doi.org/10.1021/j100785a001. NOTE - there are some variations to 
+    # the halogens in Table V that we might want to consider in the future.
+    "bondi": {
+        "H": 1.20, "He": 1.40, "C": 1.70, "N": 1.55, "O": 1.52, "F": 1.47, 
+        "Ne": 1.54, "Si": 2.10, "P": 1.80, "S": 1.80, "Cl": 1.75, "Ar": 1.88,
+        "As": 1.85, "Se": 1.90, "Br": 1.85, "Kr": 2.02, "Te": 2.06, "I": 1.98,
+        "Xe": 2.16}
+}
 
 # Numbers of valence electrons for the groups of the periodic table
 VALENCE_BY_GROUP = {1: 1, 2: 2, 13: 3, 14: 4, 15: 5, 16: 6, 17: 7, 18: 8}
diff --git a/pdb2pqr/pdb2pqr/ligand/mol2.py b/pdb2pqr/pdb2pqr/ligand/mol2.py
index d42222106..e2c4ad820 100644
--- a/pdb2pqr/pdb2pqr/ligand/mol2.py
+++ b/pdb2pqr/pdb2pqr/ligand/mol2.py
@@ -8,7 +8,9 @@ from collections import OrderedDict
 from itertools import combinations
 from numpy import array
 from numpy.linalg import norm
+from . import peoe
 from . import VALENCE_BY_ELEMENT, NONBONDED_BY_TYPE
+from . import RADII
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -105,6 +107,35 @@ class Mol2Atom:
         )
         return pdb_fmt.format(a=self)
 
+    def assign_radius(self, primary_dict, secondary_dict):
+        """Assign radius to atom.
+
+        TODO - it seems inconsistent that this function pulls radii from a 
+        dictionary and the protein routines use force field files.
+
+        Args:
+            primary_dict:  primary dictionary of radii indexed by atom type or
+                           element
+            secondary_dict:  backup dictionary for radii not found in primary
+                             dictionary
+        """
+        radius = None
+        for rdict in [primary_dict, secondary_dict]:
+            if radius is not None:
+                break
+            for key in [self.type, self.element]:
+                if key in rdict:
+                    radius = rdict[key]
+                    break
+        if radius is not None:
+            self.radius = radius
+        else:
+            err = (
+                "Unable to find radius parameter for self of type {type} in "
+                "radius dictionary: {ff}").format(
+                    type=self.type, ff=primary_dict)
+            raise KeyError(err)
+
     @property
     def coords(self):
         """Return coordinates as numpy vector."""
@@ -219,6 +250,38 @@ class Mol2Molecule:
         self.res_name = None
         self.res_seq = None
 
+    def assign_parameters(
+        self, primary_dict=RADII["zap9"], secondary_dict=RADII["bondi"]):
+        """Assign charges and radii to atoms in molecule.
+
+        Args:
+            primary_dict:  primary dictionary of radii indexed by atom type or
+                           element
+            secondary_dict:  backup dictionary for radii not found in primary
+                             dictionary
+        """
+        self.assign_radii(primary_dict, secondary_dict)
+        self.assign_charges()
+
+    def assign_radii(
+        self, primary_dict, secondary_dict):
+        """Assign radii to atoms in molecule.
+
+        Args:
+            primary_dict:  primary dictionary of radii indexed by atom type or
+                           element
+            secondary_dict:  backup dictionary for radii not found in primary
+                             dictionary
+        """
+        for atom in self.atoms.values():
+            atom.assign_radius(primary_dict, secondary_dict)
+
+    def assign_charges(self):
+        """Assign charges to atoms in molecule."""
+        for atom in self.atoms.values():
+            atom.charge = atom.formal_charge
+        peoe.equilibrate(self.atoms.values())
+
     def find_atom_torsions(self, start_atom):
         """Set the torsion angles that start with this atom (name).
 
diff --git a/pdb2pqr/pdb2pqr/ligand/parameterize.py b/pdb2pqr/pdb2pqr/ligand/parameterize.py
deleted file mode 100644
index 32e4af26f..000000000
--- a/pdb2pqr/pdb2pqr/ligand/parameterize.py
+++ /dev/null
@@ -1,52 +0,0 @@
-"""Calculating and assigning ligand charges and radii."""
-import logging
-from .mol2 import Mol2Molecule
-from .peoe import equilibrate
-from . import PARSE_RADII
-from ..forcefield import ForcefieldAtom
-from ..forcefield import ForcefieldResidue
-
-
-_LOGGER = logging.getLogger(__name__)
-
-
-class ParameterizedMolecule(Mol2Molecule):
-    """Ligand with charge and radius assignments."""
-
-    def __init__(self):
-        super().__init__()
-        self.ligand_properties = {}
-
-    def update(self, ligand):
-        """Update self with latest version of ligand (if needed).
-
-        Args:
-            ligand:  latest version of ligand
-        """
-        prev_atom_names = set(self.ligand_properties)
-        curr_atom_names = set(self.atoms)
-        if len(prev_atom_names ^ curr_atom_names) > 0:
-            self.reparameterize(ligand)
-
-    def reparameterize(self, ligand):
-        """Reassign parameters given new ligand.
-
-        Args:
-            ligand:  latest version of ligand
-        """
-        self.ligand_properties = {}
-        for atom in ligand.atoms.values():
-            atom.charge = atom.formal_charge
-        equilibrate(ligand.atoms.values())
-        for atom in ligand.atoms.values():
-            elem = atom.element.capitalize()
-            charge = atom.charge
-            try:
-                radius = PARSE_RADII[elem]
-                atom.radius = radius
-            except KeyError:
-                raise KeyError(
-                    "Unable to assign radius for element %s in atom %s" % (
-                        elem, atom))
-            self.ligand_properties[atom.name] = {
-                "charge": charge, "radius": radius}
diff --git a/pdb2pqr/pdb2pqr/main.py b/pdb2pqr/pdb2pqr/main.py
index 3f11df080..89752e3c8 100644
--- a/pdb2pqr/pdb2pqr/main.py
+++ b/pdb2pqr/pdb2pqr/main.py
@@ -20,7 +20,7 @@ from . import hydrogens
 from . import forcefield
 from . import protein as prot
 from . import input_output as io 
-from .ligand.parameterize import ParameterizedMolecule
+from .ligand.mol2 import Mol2Molecule
 from . import input_output as io
 from .config import VERSION, TITLE_FORMAT_STRING, CITATIONS, FORCE_FIELDS
 from .config import REPAIR_LIMIT
@@ -263,7 +263,7 @@ def setup_molecule(pdblist, definition, ligand_path):
         ligand:  ligand object (may be None)
     """
     if ligand_path is not None:
-        ligand = ParameterizedMolecule()
+        ligand = Mol2Molecule()
         with open(ligand_path, "rt", encoding="utf-8") as ligand_file:
             ligand.read(ligand_file)
         raise NotImplementedError("Where do initial ligand charges come from?")
diff --git a/pdb2pqr/tests/ligand_results.py b/pdb2pqr/tests/ligand_results.py
index 45f9004d8..dc6f7e316 100644
--- a/pdb2pqr/tests/ligand_results.py
+++ b/pdb2pqr/tests/ligand_results.py
@@ -88,483 +88,439 @@ FORMAL_CHARGE_RESULTS = {
     "tetramethylammonium.mol2": 4*[0] + [1] + 12*[0]
 }
 
-
-PARTIAL_CHARGE_RESULTS = {
+PARAMETER_RESULTS = {
     "1HPX-ligand.mol2": [
-        {'name': 'C1', 'charge': -0.043081773453678196},
-        {'name': 'N1', 'charge': -0.35678069534508244},
-        {'name': 'O1', 'charge': -0.5711988943947174},
-        {'name': 'S1', 'charge': -0.36230725415046},
-        {'name': 'C2', 'charge': -0.07546448002333427},
-        {'name': 'N2', 'charge': -0.703336840791423},
-        {'name': 'O2', 'charge': -0.5909676444057169},
-        {'name': 'S2', 'charge': -0.31326568130416904},
-        {'name': 'C3', 'charge': 0.012184036151037315},
-        {'name': 'N3', 'charge': -0.7139711103762134},
-        {'name': 'O3', 'charge': -0.2919660371248733},
-        {'name': 'C4', 'charge': -0.024891112570323084},
-        {'name': 'N4', 'charge': -0.7120419698971743},
-        {'name': 'O4', 'charge': -0.2689251910425875},
-        {'name': 'C5', 'charge': -0.02721768449096584},
-        {'name': 'N5', 'charge': -0.7179288700589408},
-        {'name': 'O5', 'charge': -0.2884010361503686},
-        {'name': 'C6', 'charge': 0.0753432557874654},
-        {'name': 'O6', 'charge': -0.2912545916584642},
-        {'name': 'C7', 'charge': -0.06673754373256466},
-        {'name': 'C8', 'charge': -0.11391059914410395},
-        {'name': 'C9', 'charge': -0.10324637080138911},
-        {'name': 'C10', 'charge': 0.0955779782243598},
-        {'name': 'C11', 'charge': 0.13325937240601735},
-        {'name': 'C12', 'charge': -0.007454479991213576},
-        {'name': 'C13', 'charge': 0.1300074666489752},
-        {'name': 'C14', 'charge': 0.03316079200653884},
-        {'name': 'C15', 'charge': 0.1162788489650129},
-        {'name': 'C16', 'charge': -0.05012048448800629},
-        {'name': 'C17', 'charge': 0.17629988149001455},
-        {'name': 'C18', 'charge': 0.1273124481017021},
-        {'name': 'C19', 'charge': 0.009718364614545697},
-        {'name': 'C20', 'charge': 0.05373224349483613},
-        {'name': 'C21', 'charge': 0.14236781888812639},
-        {'name': 'C22', 'charge': -0.018858356195459093},
-        {'name': 'C23', 'charge': -0.08872387572707603},
-        {'name': 'C24', 'charge': -0.08872387572707603},
-        {'name': 'C25', 'charge': -0.08872387572707603},
-        {'name': 'C26', 'charge': 0.10593153852032608},
-        {'name': 'C27', 'charge': -0.05782750620937734},
-        {'name': 'C28', 'charge': -0.09940049289330599},
-        {'name': 'C29', 'charge': -0.11788247675515531},
-        {'name': 'C30', 'charge': -0.12669321002628098},
-        {'name': 'C31', 'charge': -0.12840215383108972},
-        {'name': 'C32', 'charge': -0.12669321002628098},
-        {'name': 'C33', 'charge': -0.11788247675515531},
-        {'name': 'HN2', 'charge': 0.47365062709293504},
-        {'name': 'HN3', 'charge': 0.46813799183459115},
-        {'name': 'HN5', 'charge': 0.4699450251195792},
-        {'name': 'HO2', 'charge': 0.4135083335659837},
-        {'name': 'H1', 'charge': 0.1930651515377243},
-        {'name': 'H2', 'charge': 0.14930498376978826},
-        {'name': 'H5', 'charge': 0.2004887586723136},
-        {'name': 'H7', 'charge': 0.1568207646303434},
-        {'name': 'H8', 'charge': 0.13234810374569977},
-        {'name': 'H9', 'charge': 0.13832988708343302},
-        {'name': '1H10', 'charge': 0.2090610332096663},
-        {'name': '2H10', 'charge': 0.2090610332096663},
-        {'name': '1H12', 'charge': 0.12111462041395545},
-        {'name': '2H12', 'charge': 0.12111462041395545},
-        {'name': 'H14', 'charge': 0.1675599590015787},
-        {'name': 'H15', 'charge': 0.22760838606623204},
-        {'name': '1H16', 'charge': 0.0852867334715187},
-        {'name': '2H16', 'charge': 0.0852867334715187},
-        {'name': 'H18', 'charge': 0.24317031751195953},
-        {'name': '1H19', 'charge': 0.12776560931027464},
-        {'name': '2H19', 'charge': 0.12776560931027464},
-        {'name': '1H20', 'charge': 0.19565330098691133},
-        {'name': '2H20', 'charge': 0.19565330098691133},
-        {'name': '1H23', 'charge': 0.05671902293773316},
-        {'name': '2H23', 'charge': 0.05671902293773316},
-        {'name': '3H23', 'charge': 0.05671902293773316},
-        {'name': '1H24', 'charge': 0.05671902293773316},
-        {'name': '2H24', 'charge': 0.05671902293773316},
-        {'name': '3H24', 'charge': 0.05671902293773316},
-        {'name': '1H25', 'charge': 0.05671902293773316},
-        {'name': '2H25', 'charge': 0.05671902293773316},
-        {'name': '3H25', 'charge': 0.05671902293773316},
-        {'name': 'H26', 'charge': 0.21276929701184144},
-        {'name': '1H27', 'charge': 0.0838296767957033},
-        {'name': '2H27', 'charge': 0.0838296767957033},
-        {'name': '3H27', 'charge': 0.0838296767957033},
-        {'name': 'H29', 'charge': 0.1344214537548114},
-        {'name': 'H30', 'charge': 0.12944135663694809},
-        {'name': 'H31', 'charge': 0.12895177093126134},
-        {'name': 'H32', 'charge': 0.12944135663694809},
-        {'name': 'H33', 'charge': 0.1344214537548114}],
+        {'name': 'C1', 'type': 'C.ar', 'charge': -0.043081773453678196, 'radius': 1.87},
+        {'name': 'N1', 'type': 'N.ar', 'charge': -0.35678069534508244, 'radius': 1.4},
+        {'name': 'O1', 'type': 'O.3', 'charge': -0.5711988943947174, 'radius': 1.52},
+        {'name': 'S1', 'type': 'S.3', 'charge': -0.36230725415046, 'radius': 2.15},
+        {'name': 'C2', 'type': 'C.ar', 'charge': -0.07546448002333427, 'radius': 1.87},
+        {'name': 'N2', 'type': 'N.am', 'charge': -0.703336840791423, 'radius': 1.4},
+        {'name': 'O2', 'type': 'O.3', 'charge': -0.5909676444057169, 'radius': 1.52},
+        {'name': 'S2', 'type': 'S.3', 'charge': -0.31326568130416904, 'radius': 2.15},
+        {'name': 'C3', 'type': 'C.ar', 'charge': 0.012184036151037315, 'radius': 1.87},
+        {'name': 'N3', 'type': 'N.am', 'charge': -0.7139711103762134, 'radius': 1.4},
+        {'name': 'O3', 'type': 'O.2', 'charge': -0.2919660371248733, 'radius': 1.52},
+        {'name': 'C4', 'type': 'C.ar', 'charge': -0.024891112570323084, 'radius': 1.87},
+        {'name': 'N4', 'type': 'N.am', 'charge': -0.7120419698971743, 'radius': 1.4},
+        {'name': 'O4', 'type': 'O.2', 'charge': -0.2689251910425875, 'radius': 1.52},
+        {'name': 'C5', 'type': 'C.ar', 'charge': -0.02721768449096584, 'radius': 1.87},
+        {'name': 'N5', 'type': 'N.am', 'charge': -0.7179288700589408, 'radius': 1.4},
+        {'name': 'O5', 'type': 'O.2', 'charge': -0.2884010361503686, 'radius': 1.52},
+        {'name': 'C6', 'type': 'C.ar', 'charge': 0.0753432557874654, 'radius': 1.87},
+        {'name': 'O6', 'type': 'O.2', 'charge': -0.2912545916584642, 'radius': 1.52},
+        {'name': 'C7', 'type': 'C.ar', 'charge': -0.06673754373256466, 'radius': 1.87},
+        {'name': 'C8', 'type': 'C.ar', 'charge': -0.11391059914410395, 'radius': 1.87},
+        {'name': 'C9', 'type': 'C.ar', 'charge': -0.10324637080138911, 'radius': 1.87},
+        {'name': 'C10', 'type': 'C.3', 'charge': 0.0955779782243598, 'radius': 1.87},
+        {'name': 'C11', 'type': 'C.2', 'charge': 0.13325937240601735, 'radius': 1.87},
+        {'name': 'C12', 'type': 'C.3', 'charge': -0.007454479991213576, 'radius': 1.87},
+        {'name': 'C13', 'type': 'C.2', 'charge': 0.1300074666489752, 'radius': 1.87},
+        {'name': 'C14', 'type': 'C.3', 'charge': 0.03316079200653884, 'radius': 1.87},
+        {'name': 'C15', 'type': 'C.3', 'charge': 0.1162788489650129, 'radius': 1.87},
+        {'name': 'C16', 'type': 'C.3', 'charge': -0.05012048448800629, 'radius': 1.87},
+        {'name': 'C17', 'type': 'C.2', 'charge': 0.17629988149001455, 'radius': 1.87},
+        {'name': 'C18', 'type': 'C.3', 'charge': 0.1273124481017021, 'radius': 1.87},
+        {'name': 'C19', 'type': 'C.3', 'charge': 0.009718364614545697, 'radius': 1.87},
+        {'name': 'C20', 'type': 'C.3', 'charge': 0.05373224349483613, 'radius': 1.87},
+        {'name': 'C21', 'type': 'C.2', 'charge': 0.14236781888812639, 'radius': 1.87},
+        {'name': 'C22', 'type': 'C.3', 'charge': -0.018858356195459093, 'radius': 1.87},
+        {'name': 'C23','type': 'C.3', 'charge': -0.08872387572707603, 'radius': 1.87},
+        {'name': 'C24', 'type': 'C.3', 'charge': -0.08872387572707603, 'radius': 1.87},
+        {'name': 'C25', 'type': 'C.3', 'charge': -0.08872387572707603, 'radius': 1.87},
+        {'name': 'C26', 'type': 'C.3', 'charge': 0.10593153852032608, 'radius': 1.87},
+        {'name': 'C27', 'type': 'C.3', 'charge': -0.05782750620937734, 'radius': 1.87},
+        {'name': 'C28', 'type': 'C.ar', 'charge': -0.09940049289330599, 'radius': 1.87},
+        {'name': 'C29', 'type': 'C.ar', 'charge': -0.11788247675515531, 'radius': 1.87},
+        {'name': 'C30', 'type': 'C.ar', 'charge': -0.12669321002628098, 'radius': 1.87},
+        {'name': 'C31', 'type': 'C.ar', 'charge': -0.12840215383108972, 'radius': 1.87},
+        {'name': 'C32', 'type': 'C.ar', 'charge': -0.12669321002628098, 'radius': 1.87},
+        {'name': 'C33', 'type': 'C.ar', 'charge': -0.11788247675515531, 'radius': 1.87},
+        {'name': 'HN2', 'type': 'H', 'charge': 0.47365062709293504, 'radius': 1.1},
+        {'name': 'HN3', 'type': 'H', 'charge': 0.46813799183459115, 'radius': 1.1},
+        {'name': 'HN5', 'type': 'H', 'charge': 0.4699450251195792, 'radius': 1.1},
+        {'name': 'HO2', 'type': 'H', 'charge': 0.4135083335659837, 'radius': 1.1},
+        {'name':'H1', 'type': 'H', 'charge': 0.1930651515377243, 'radius': 1.1},
+        {'name': 'H2', 'type': 'H', 'charge': 0.14930498376978826, 'radius': 1.1},
+        {'name': 'H5', 'type': 'H', 'charge': 0.2004887586723136, 'radius': 1.1},
+        {'name': 'H7', 'type': 'H', 'charge': 0.1568207646303434, 'radius': 1.1},
+        {'name': 'H8', 'type': 'H', 'charge': 0.13234810374569977, 'radius': 1.1},
+        {'name': 'H9', 'type': 'H', 'charge': 0.13832988708343302, 'radius': 1.1},
+        {'name': '1H10', 'type': 'H', 'charge': 0.2090610332096663, 'radius': 1.1},
+        {'name': '2H10', 'type': 'H', 'charge': 0.2090610332096663, 'radius': 1.1},
+        {'name': '1H12', 'type': 'H', 'charge': 0.12111462041395545, 'radius': 1.1},
+        {'name': '2H12', 'type': 'H', 'charge': 0.12111462041395545, 'radius': 1.1},
+        {'name': 'H14', 'type': 'H', 'charge': 0.1675599590015787, 'radius': 1.1},
+        {'name': 'H15', 'type': 'H', 'charge': 0.22760838606623204, 'radius': 1.1},
+        {'name': '1H16', 'type': 'H', 'charge': 0.0852867334715187, 'radius': 1.1},
+        {'name': '2H16', 'type': 'H', 'charge': 0.0852867334715187, 'radius': 1.1},
+        {'name': 'H18', 'type': 'H', 'charge': 0.24317031751195953, 'radius': 1.1},
+        {'name': '1H19', 'type': 'H', 'charge': 0.12776560931027464, 'radius': 1.1},
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+        {'name': 'CAA', 'type': 'C.3', 'charge': -0.10295775116564801, 'radius': 1.87},
+        {'name': 'HAA', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'HAB', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'CAB', 'type': 'C.3', 'charge': -0.10295775116564801, 'radius': 1.87},
+        {'name': 'HAC', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'HAD', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'CAC', 'type': 'C.3', 'charge': -0.10295775116564801, 'radius': 1.87},
+        {'name': 'HAE', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'HAF', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'CAF', 'type': 'C.3', 'charge': -0.10295775116564801, 'radius': 1.87},
+        {'name': 'HAK', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'HAL', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'CAE', 'type': 'C.3', 'charge': -0.10295775116564801, 'radius': 1.87},
+        {'name': 'HAI', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'HAJ', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'CAD', 'type': 'C.3', 'charge': -0.10295775116564801, 'radius': 1.87},
+        {'name': 'HAH', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1},
+        {'name': 'HAG', 'type': 'H', 'charge': 0.051478875582824005, 'radius': 1.1}],
     "ethanol.mol2": [
-        {'name': 'CAA', 'charge': -0.09830853015557071},
-        {'name': 'HAA', 'charge': 0.04965533009730527},
-        {'name': 'HAB', 'charge': 0.04965533009730527},
-        {'name': 'HAC', 'charge': 0.04965533009730527},
-        {'name': 'CAB', 'charge': -0.05333201263132795},
-        {'name': 'HAD', 'charge': 0.1136006498229285},
-        {'name': 'HAE', 'charge': 0.1136006498229285},
-        {'name': 'OAC', 'charge': -0.6256712436819194},
-        {'name': 'HAF', 'charge': 0.4011444965310452}],
+        {'name': 'CAA', 'type': 'C.3', 'charge': -0.09830853015557071, 'radius': 1.87},
+        {'name': 'HAA', 'type': 'H', 'charge': 0.04965533009730527, 'radius': 1.1},
+        {'name': 'HAB', 'type': 'H', 'charge': 0.04965533009730527, 'radius': 1.1},
+        {'name': 'HAC', 'type': 'H', 'charge': 0.04965533009730527, 'radius': 1.1},
+        {'name': 'CAB', 'type': 'C.3', 'charge': -0.05333201263132795, 'radius': 1.87},
+        {'name': 'HAD', 'type': 'H', 'charge': 0.1136006498229285, 'radius': 1.1},
+        {'name': 'HAE', 'type': 'H', 'charge': 0.1136006498229285, 'radius': 1.1},
+        {'name': 'OAC', 'type': 'O.3', 'charge': -0.6256712436819194, 'radius': 1.52},
+        {'name': 'HAF', 'type': 'H', 'charge': 0.4011444965310452, 'radius': 1.1}],
     "fatty-acid.mol2": [
-        {'name': 'OAA', 'charge': -0.6905415761361866},
-        {'name': 'CAB', 'charge': 0.09491530638614049},
-        {'name': 'OAL', 'charge': -0.6905415761361866},
-        {'name': 'CAC', 'charge': 0.012573264939255872},
-        {'name': 'HAC', 'charge': 0.11848768797200306},
-        {'name': 'HAD', 'charge': 0.11848768797200306},
-        {'name': 'CAD', 'charge': -0.07742980670292797},
-        {'name': 'HAE', 'charge': 0.06140059278092227},
-        {'name': 'HAF', 'charge': 0.06140059278092227},
-        {'name': 'CAE', 'charge': -0.076959643935905},
-        {'name': 'HAG', 'charge': 0.07285165771612633},
-        {'name': 'HAH', 'charge': 0.07285165771612633},
-        {'name': 'CAF', 'charge': -0.24236491728150775},
-        {'name': 'HAI', 'charge': 0.16485599597989423},
-        {'name': 'CAG', 'charge': -0.2426026937449157},
-        {'name': 'HAJ', 'charge': 0.1648388876026803},
-        {'name': 'CAH', 'charge': -0.07965667787077134},
-        {'name': 'HAK', 'charge': 0.07232360507910963},
-        {'name': 'HAL', 'charge': 0.07232360507910963},
-        {'name': 'CAI', 'charge': -0.09862724378017657},
-        {'name': 'HAM', 'charge': 0.05403847507524275},
-        {'name': 'HAN', 'charge': 0.05403847507524275},
-        {'name': 'CAJ', 'charge': -0.10608184708836539},
-        {'name': 'HAO', 'charge': 0.04966180988232633},
-        {'name': 'HAP', 'charge': 0.04966180988232633},
-        {'name': 'CAK', 'charge': -0.11173869603286389},
-        {'name': 'HAR', 'charge': 0.04061118893012504},
-        {'name': 'HAS', 'charge': 0.04061118893012504},
-        {'name': 'HAQ', 'charge': 0.04061118893012504}],
+        {'name': 'OAA', 'type': 'O.co2', 'charge': -0.6905415761361866, 'radius': 1.76},
+        {'name': 'CAB', 'type': 'C.2', 'charge': 0.09491530638614049, 'radius': 1.87},
+        {'name': 'OAL', 'type': 'O.co2', 'charge': -0.6905415761361866, 'radius': 1.76},
+        {'name': 'CAC', 'type': 'C.3', 'charge': 0.012573264939255872, 'radius': 1.87},
+        {'name': 'HAC', 'type': 'H', 'charge': 0.11848768797200306, 'radius': 1.1},
+        {'name': 'HAD', 'type': 'H', 'charge': 0.11848768797200306, 'radius': 1.1},
+        {'name': 'CAD', 'type': 'C.3', 'charge': -0.07742980670292797, 'radius': 1.87},
+        {'name': 'HAE', 'type': 'H', 'charge': 0.06140059278092227, 'radius': 1.1},
+        {'name': 'HAF', 'type': 'H', 'charge': 0.06140059278092227, 'radius': 1.1},
+        {'name': 'CAE', 'type': 'C.3', 'charge': -0.076959643935905, 'radius': 1.87},
+        {'name': 'HAG', 'type': 'H', 'charge': 0.07285165771612633, 'radius': 1.1},
+        {'name': 'HAH', 'type': 'H', 'charge': 0.07285165771612633, 'radius': 1.1},
+        {'name': 'CAF', 'type': 'C.2', 'charge': -0.24236491728150775, 'radius': 1.87},
+        {'name': 'HAI', 'type': 'H', 'charge': 0.16485599597989423, 'radius': 1.1},
+        {'name': 'CAG', 'type': 'C.2', 'charge': -0.2426026937449157, 'radius': 1.87},
+        {'name': 'HAJ', 'type': 'H', 'charge': 0.1648388876026803, 'radius': 1.1},
+        {'name': 'CAH', 'type': 'C.3', 'charge': -0.07965667787077134, 'radius': 1.87},
+        {'name': 'HAK', 'type': 'H', 'charge': 0.07232360507910963, 'radius': 1.1},
+        {'name': 'HAL', 'type': 'H', 'charge': 0.07232360507910963, 'radius': 1.1},
+        {'name': 'CAI', 'type': 'C.3', 'charge': -0.09862724378017657, 'radius': 1.87},
+        {'name': 'HAM', 'type': 'H', 'charge': 0.05403847507524275, 'radius': 1.1},
+        {'name': 'HAN', 'type': 'H', 'charge': 0.05403847507524275, 'radius': 1.1},
+        {'name': 'CAJ', 'type': 'C.3', 'charge': -0.10608184708836539, 'radius': 1.87},
+        {'name': 'HAO', 'type': 'H', 'charge': 0.04966180988232633, 'radius': 1.1},
+        {'name': 'HAP', 'type': 'H', 'charge': 0.04966180988232633, 'radius': 1.1},
+        {'name': 'CAK', 'type': 'C.3', 'charge': -0.11173869603286389, 'radius': 1.87},
+        {'name': 'HAR', 'type': 'H', 'charge': 0.04061118893012504, 'radius': 1.1},
+        {'name': 'HAS', 'type': 'H', 'charge': 0.04061118893012504, 'radius': 1.1},
+        {'name': 'HAQ', 'type': 'H', 'charge': 0.04061118893012504, 'radius': 1.1}],
     "glycerol.mol2": [
-        {'name': 'OAB', 'charge': -0.6193219106971865},
-        {'name': 'HAG', 'charge': 0.4033320347133161},
-        {'name': 'CAA', 'charge': -0.025227212803925057},
-        {'name': 'HAA', 'charge': 0.1316040991547254},
-        {'name': 'HAB', 'charge': 0.1316040991547254},
-        {'name': 'CAC', 'charge': -0.00300604112002907},
-        {'name': 'HAC', 'charge': 0.16288785945019288},
-        {'name': 'OAD', 'charge': -0.6115908338990877},
-        {'name': 'HAD', 'charge': 0.4077267965256133},
-        {'name': 'CAE', 'charge': -0.025227212803925054},
-        {'name': 'HAE', 'charge': 0.1316040991547254},
-        {'name': 'HAF', 'charge': 0.1316040991547254},
-        {'name': 'OAF', 'charge': -0.6193219106971865},
-        {'name': 'HAH', 'charge': 0.4033320347133161}],
+        {'name': 'OAB', 'type': 'O.3', 'charge': -0.6193219106971865, 'radius': 1.52},
+        {'name': 'HAG', 'type': 'H', 'charge': 0.4033320347133161, 'radius': 1.1},
+        {'name': 'CAA', 'type': 'C.3', 'charge': -0.025227212803925057, 'radius': 1.87},
+        {'name': 'HAA', 'type': 'H', 'charge': 0.1316040991547254, 'radius': 1.1},
+        {'name': 'HAB', 'type': 'H', 'charge': 0.1316040991547254, 'radius': 1.1},
+        {'name': 'CAC', 'type': 'C.3', 'charge': -0.00300604112002907, 'radius': 1.87},
+        {'name': 'HAC', 'type': 'H', 'charge': 0.16288785945019288, 'radius': 1.1},
+        {'name': 'OAD', 'type': 'O.3', 'charge': -0.6115908338990877, 'radius': 1.52},
+        {'name': 'HAD', 'type': 'H', 'charge': 0.4077267965256133, 'radius': 1.1},
+        {'name': 'CAE', 'type': 'C.3', 'charge': -0.025227212803925054, 'radius': 1.87},
+        {'name': 'HAE', 'type': 'H', 'charge': 0.1316040991547254, 'radius': 1.1},
+        {'name': 'HAF', 'type': 'H', 'charge': 0.1316040991547254, 'radius': 1.1},
+        {'name': 'OAF', 'type': 'O.3', 'charge': -0.6193219106971865, 'radius': 1.52},
+        {'name': 'HAH', 'type': 'H', 'charge': 0.4033320347133161, 'radius': 1.1}],
     "naphthalene.mol2": [
-        {'name': 'CAB', 'charge': -0.10985826436427909},
-        {'name': 'HAB', 'charge': 0.13714843913419308},
-        {'name': 'CAC', 'charge': -0.06352790423000582},
-        {'name': 'CAD', 'charge': -0.10985826436427909},
-        {'name': 'HAD', 'charge': 0.13714843913419308},
-        {'name': 'CAE', 'charge': -0.12522022371734542},
-        {'name': 'HAE', 'charge': 0.1296940010624343},
-        {'name': 'CAJ', 'charge': -0.12522022371734542},
-        {'name': 'HAJ', 'charge': 0.1296940010624343},
-        {'name': 'CAI', 'charge': -0.10985826436427909},
-        {'name': 'HAI', 'charge': 0.13714843913419308},
-        {'name': 'CAH', 'charge': -0.06352790423000582},
-        {'name': 'CAG', 'charge': -0.10985826436427909},
-        {'name': 'HAG', 'charge': 0.13714843913419308},
-        {'name': 'CAF', 'charge': -0.12522022371734542},
-        {'name': 'HAF', 'charge': 0.1296940010624343},
-        {'name': 'CAA', 'charge': -0.12522022371734542},
-        {'name': 'HAA', 'charge': 0.1296940010624343}],
+        {'name': 'CAB', 'type': 'C.ar', 'charge': -0.10985826436427909, 'radius': 1.87},
+        {'name': 'HAB', 'type': 'H', 'charge': 0.13714843913419308, 'radius': 1.1},
+        {'name': 'CAC', 'type': 'C.ar', 'charge': -0.06352790423000582, 'radius': 1.87},
+        {'name': 'CAD', 'type': 'C.ar', 'charge': -0.10985826436427909, 'radius': 1.87},
+        {'name': 'HAD', 'type': 'H', 'charge': 0.13714843913419308, 'radius': 1.1},
+        {'name': 'CAE', 'type': 'C.ar', 'charge': -0.12522022371734542, 'radius': 1.87},
+        {'name': 'HAE', 'type': 'H', 'charge': 0.1296940010624343, 'radius': 1.1},
+        {'name': 'CAJ', 'type': 'C.ar', 'charge': -0.12522022371734542, 'radius': 1.87},
+        {'name': 'HAJ', 'type': 'H', 'charge': 0.1296940010624343, 'radius': 1.1},
+        {'name': 'CAI', 'type': 'C.ar', 'charge': -0.10985826436427909, 'radius': 1.87},
+        {'name': 'HAI', 'type': 'H', 'charge': 0.13714843913419308, 'radius': 1.1},
+        {'name': 'CAH', 'type': 'C.ar', 'charge': -0.06352790423000582, 'radius': 1.87},
+        {'name': 'CAG', 'type': 'C.ar', 'charge': -0.10985826436427909, 'radius': 1.87},
+        {'name': 'HAG', 'type': 'H', 'charge': 0.13714843913419308, 'radius': 1.1},
+        {'name': 'CAF', 'type': 'C.ar', 'charge': -0.12522022371734542, 'radius': 1.87},
+        {'name': 'HAF', 'type': 'H', 'charge': 0.1296940010624343, 'radius': 1.1},
+        {'name': 'CAA', 'type': 'C.ar', 'charge': -0.12522022371734542, 'radius': 1.87},
+        {'name': 'HAA', 'type': 'H', 'charge': 0.1296940010624343, 'radius': 1.1}],
     "pyrrole.mol2": [
-        {'name': 'CAE', 'charge': -0.02725132001441914},
-        {'name': 'HAE', 'charge': 0.104834463409739},
-        {'name': 'HAF', 'charge': 0.104834463409739},
-        {'name': 'CAD', 'charge': -0.19753848158167037},
-        {'name': 'HAD', 'charge': 0.18534981863154645},
-        {'name': 'CAA', 'charge': -0.1112561716335608},
-        {'name': 'HAA', 'charge': 0.2699321111667989},
-        {'name': 'NAB', 'charge': -0.44475473234270757},
-        {'name': 'CAC', 'charge': -0.13358085588726296},
-        {'name': 'HAC', 'charge': 0.24943070484179752}],
+        {'name': 'CAE', 'type': 'C.3', 'charge': -0.02725132001441914, 'radius': 1.87},
+        {'name': 'HAE', 'type': 'H', 'charge': 0.104834463409739, 'radius': 1.1},
+        {'name': 'HAF', 'type': 'H', 'charge': 0.104834463409739, 'radius': 1.1},
+        {'name': 'CAD', 'type': 'C.2', 'charge': -0.19753848158167037, 'radius': 1.87},
+        {'name': 'HAD', 'type': 'H', 'charge': 0.18534981863154645, 'radius': 1.1},
+        {'name': 'CAA', 'type': 'C.2', 'charge': -0.1112561716335608, 'radius': 1.87},
+        {'name': 'HAA', 'type': 'H', 'charge': 0.2699321111667989, 'radius': 1.1},
+        {'name': 'NAB', 'type': 'N.2', 'charge': -0.44475473234270757, 'radius': 1.4},
+        {'name': 'CAC', 'type': 'C.2', 'charge': -0.13358085588726296, 'radius': 1.87},
+        {'name': 'HAC', 'type': 'H', 'charge': 0.24943070484179752, 'radius': 1.1}],
     "tetramethylammonium.mol2": [
-        {'name': 'CAA', 'charge': 0.013840200623221964},
-        {'name': 'HAA', 'charge': 0.12997929051575582},
-        {'name': 'HAB', 'charge': 0.12997929051575582},
-        {'name': 'HAC', 'charge': 0.12997929051575582},
-        {'name': 'NAC', 'charge': -0.6151122886819584},
-        {'name': 'CAB', 'charge': 0.013840200623221978},
-        {'name': 'HAE', 'charge': 0.12997929051575582},
-        {'name': 'HAF', 'charge': 0.12997929051575582},
-        {'name': 'HAD', 'charge': 0.12997929051575582},
-        {'name': 'CAE', 'charge': 0.013840200623221978},
-        {'name': 'HAK', 'charge': 0.12997929051575582},
-        {'name': 'HAL', 'charge': 0.12997929051575582},
-        {'name': 'HAJ', 'charge': 0.12997929051575582},
-        {'name': 'CAD', 'charge': 0.013840200623221978},
-        {'name': 'HAH', 'charge': 0.12997929051575582},
-        {'name': 'HAI', 'charge': 0.12997929051575582},
-        {'name': 'HAG', 'charge': 0.12997929051575582}]
+        {'name': 'CAA', 'type': 'C.3', 'charge': 0.013840200623221964, 'radius': 1.87},
+        {'name': 'HAA', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAB', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAC', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'NAC', 'type': 'N.3', 'charge': -0.6151122886819584, 'radius': 1.4},
+        {'name': 'CAB', 'type': 'C.3', 'charge': 0.013840200623221978, 'radius': 1.87},
+        {'name': 'HAE', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAF', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAD', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'CAE', 'type': 'C.3', 'charge': 0.013840200623221978, 'radius': 1.87},
+        {'name': 'HAK', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAL', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAJ', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'CAD', 'type': 'C.3', 'charge': 0.013840200623221978, 'radius': 1.87},
+        {'name': 'HAH', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAI', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1},
+        {'name': 'HAG', 'type': 'H', 'charge': 0.12997929051575582, 'radius': 1.1}]
 }
diff --git a/pdb2pqr/tests/ligand_test.py b/pdb2pqr/tests/ligand_test.py
index 83291a06a..46bd6319b 100644
--- a/pdb2pqr/tests/ligand_test.py
+++ b/pdb2pqr/tests/ligand_test.py
@@ -5,15 +5,15 @@ from pathlib import Path
 import pytest
 import pandas as pd
 from numpy.testing import assert_almost_equal
-from pdb2pqr.ligand import parameterize
+from pdb2pqr.ligand.mol2 import Mol2Molecule
+from pdb2pqr.ligand import RADII
 import common
 from ligand_results import TORSION_RESULTS, RING_RESULTS
-from ligand_results import FORMAL_CHARGE_RESULTS, PARTIAL_CHARGE_RESULTS
+from ligand_results import FORMAL_CHARGE_RESULTS, PARAMETER_RESULTS
 
 
 _LOGGER = logging.getLogger(__name__)
 _LOGGER.warning("Need functional and regression test coverage for --ligand")
-_LOGGER.error("Still haven't figured out radii")
 
 
 ALL_LIGANDS = set(TORSION_RESULTS) | set(RING_RESULTS)
@@ -24,46 +24,44 @@ ALL_LIGANDS = sorted(list(ALL_LIGANDS))
 
 
 @pytest.mark.parametrize("input_mol2", ALL_LIGANDS)
-def test_parameterization(input_mol2):
+def test_assign_parameters(input_mol2):
     """Testing basic aspects of code breaking."""
-    ligand = parameterize.ParameterizedMolecule()
+    ligand = Mol2Molecule()
     mol2_path = Path("tests/data") / input_mol2
     with open(mol2_path, "rt") as mol2_file:
         ligand.read(mol2_file)
     old_total_charge = 0
     for atom in ligand.atoms.values():
-        atom.charge = atom.formal_charge
-        old_total_charge += atom.charge
-        atom.old_charge = atom.charge
-    ligand.update(ligand)
+        old_total_charge += atom.formal_charge
+    ligand.assign_parameters()
     new_total_charge = 0
     test_results = []
     for atom in ligand.atoms.values():
         test_row = {
-            "name": atom.name, "charge": atom.charge}
+            "name": atom.name, "type": atom.type, "charge": atom.charge,
+            "radius": atom.radius}
         test_results.append(test_row)
         new_total_charge += atom.charge
     _LOGGER.debug("Test results: %s", test_results)
     test_results = pd.DataFrame(test_results)
     test_results = test_results.set_index("name")
-    _LOGGER.debug("Test results:\n%s", test_results)
+    # _LOGGER.debug("Test results:\n%s", test_results.to_string())
     _LOGGER.info(
         "Total charge: %5.2f -> %5.2f", old_total_charge, new_total_charge)
-    expected_results = pd.DataFrame(PARTIAL_CHARGE_RESULTS[input_mol2])
+    expected_results = pd.DataFrame(PARAMETER_RESULTS[input_mol2])
     expected_results = expected_results.set_index("name")
-    diff_results = test_results - expected_results
-    _LOGGER.debug(
-        "Difference between test and expected results:\n%s",
-        diff_results.to_string())
     assert_almost_equal(
         test_results["charge"].to_numpy(),
         expected_results["charge"].to_numpy())
+    assert_almost_equal(
+        test_results["radius"].to_numpy(),
+        expected_results["radius"].to_numpy(), verbose=True)
 
 
 @pytest.mark.parametrize("input_mol2", ALL_LIGANDS)
 def test_formal_charge(input_mol2):
     """Testing formal charge calculation."""
-    ligand = parameterize.ParameterizedMolecule()
+    ligand = Mol2Molecule()
     mol2_path = Path("tests/data") / input_mol2
     with open(mol2_path, "rt") as mol2_file:
         ligand.read(mol2_file)
@@ -91,7 +89,7 @@ def test_formal_charge(input_mol2):
 @pytest.mark.parametrize("input_mol2", TORSION_RESULTS)
 def test_torsions(input_mol2):
     """Test assignment of torsion angles."""
-    ligand = parameterize.ParameterizedMolecule()
+    ligand = Mol2Molecule()
     mol2_path = Path("tests/data") / input_mol2
     with open(mol2_path, "rt") as mol2_file:
         ligand.read(mol2_file)
@@ -125,7 +123,7 @@ def test_torsions(input_mol2):
 @pytest.mark.parametrize("input_mol2", ALL_LIGANDS)
 def test_rings(input_mol2):
     """Test assignment of torsion angles."""
-    ligand = parameterize.ParameterizedMolecule()
+    ligand = Mol2Molecule()
     mol2_path = Path("tests/data") / input_mol2
     with open(mol2_path, "rt") as mol2_file:
         ligand.read(mol2_file)