diff --git a/python/BioSimSpace/Parameters/_Protocol/_openforcefield.py b/python/BioSimSpace/Parameters/_Protocol/_openforcefield.py
index 7c3aed05a..018f43e4e 100644
--- a/python/BioSimSpace/Parameters/_Protocol/_openforcefield.py
+++ b/python/BioSimSpace/Parameters/_Protocol/_openforcefield.py
@@ -127,7 +127,9 @@
 class OpenForceField(_protocol.Protocol):
     """A class for handling protocols for Open Force Field models."""
 
-    def __init__(self, forcefield, ensure_compatible=True, property_map={}):
+    def __init__(
+        self, forcefield, ensure_compatible=True, use_nagl=True, property_map={}
+    ):
         """
         Constructor.
 
@@ -145,6 +147,11 @@ def __init__(self, forcefield, ensure_compatible=True, property_map={}):
             original molecule, e.g. the original atom and residue names will be
             kept.
 
+        use_nagl : bool
+            Whether to use NAGL to compute AM1-BCC charges. If False, the default
+            is to use AmberTools via antechamber and sqm. (This option is only
+            used if NAGL is available.)
+
         property_map : dict
             A dictionary that maps system "properties" to their user defined
             values. This allows the user to refer to properties with their
@@ -158,6 +165,12 @@ def __init__(self, forcefield, ensure_compatible=True, property_map={}):
             property_map=property_map,
         )
 
+        if not isinstance(use_nagl, bool):
+            raise TypeError("'use_nagl' must be of type 'bool'")
+
+        # Set the NAGL flag.
+        self._use_nagl = use_nagl
+
         # Set the compatibility flags.
         self._tleap = False
         self._pdb2gmx = False
@@ -314,7 +327,7 @@ def run(self, molecule, work_dir=None, queue=None):
                     raise _ThirdPartyError(msg) from None
 
         # Apply AM1-BCC charges using NAGL.
-        if _has_nagl:
+        if _has_nagl and self._use_nagl:
             try:
                 _nagl.assign_partial_charges(
                     off_molecule, partial_charge_method=_nagl_model
diff --git a/python/BioSimSpace/Parameters/_parameters.py b/python/BioSimSpace/Parameters/_parameters.py
index 07a49d24b..6e8570bb9 100644
--- a/python/BioSimSpace/Parameters/_parameters.py
+++ b/python/BioSimSpace/Parameters/_parameters.py
@@ -463,6 +463,7 @@ def _parameterise_openff(
     forcefield,
     molecule,
     ensure_compatible=True,
+    use_nagl=True,
     work_dir=None,
     property_map={},
     **kwargs,
@@ -489,6 +490,11 @@ def _parameterise_openff(
         the parameterised molecule will preserve the topology of the original
         molecule, e.g. the original atom and residue names will be kept.
 
+    use_nagl : bool
+        Whether to use NAGL to compute AM1-BCC charges. If False, the default
+        is to use AmberTools via antechamber and sqm. (This option is only
+        used if NAGL is available.)
+
     work_dir : str
         The working directory for the process.
 
@@ -583,12 +589,21 @@ def _parameterise_openff(
         if forcefield not in _forcefields_lower:
             raise ValueError("Supported force fields are: %s" % openForceFields())
 
+    if not isinstance(ensure_compatible, bool):
+        raise TypeError("'ensure_compatible' must be of type 'bool'.")
+
+    if not isinstance(use_nagl, bool):
+        raise TypeError("'use_nagl' must be of type 'bool'.")
+
     if not isinstance(property_map, dict):
         raise TypeError("'property_map' must be of type 'dict'")
 
     # Create a default protocol.
     protocol = _Protocol.OpenForceField(
-        forcefield, ensure_compatible=ensure_compatible, property_map=property_map
+        forcefield,
+        ensure_compatible=ensure_compatible,
+        use_nagl=use_nagl,
+        property_map=property_map,
     )
 
     # Run the parameterisation protocol in the background and return
@@ -1079,7 +1094,9 @@ def _function(
 # it conforms to sensible function naming standards, i.e. "-" and "."
 # characters replaced by underscores.
 def _make_openff_function(name):
-    def _function(molecule, ensure_compatible=True, work_dir=None, property_map={}):
+    def _function(
+        molecule, ensure_compatible=True, use_nagl=True, work_dir=None, property_map={}
+    ):
         """
         Parameterise a molecule using the named force field from the
         Open Force Field initiative.
@@ -1100,6 +1117,11 @@ def _function(molecule, ensure_compatible=True, work_dir=None, property_map={}):
             molecule will preserve the topology of the original molecule, e.g.
             the original atom and residue names will be kept.
 
+        use_nagl : bool
+            Whether to use NAGL to compute AM1-BCC charges. If False, the default
+            is to use AmberTools via antechamber and sqm. (This option is only
+            used if NAGL is available.)
+
         work_dir : str
             The working directory for the process.
 
@@ -1118,6 +1140,7 @@ def _function(molecule, ensure_compatible=True, work_dir=None, property_map={}):
             name,
             molecule,
             ensure_compatible=ensure_compatible,
+            use_nagl=use_nagl,
             work_dir=work_dir,
             property_map=property_map,
         )
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_openforcefield.py b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_openforcefield.py
index 7c3aed05a..018f43e4e 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_openforcefield.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_Protocol/_openforcefield.py
@@ -127,7 +127,9 @@
 class OpenForceField(_protocol.Protocol):
     """A class for handling protocols for Open Force Field models."""
 
-    def __init__(self, forcefield, ensure_compatible=True, property_map={}):
+    def __init__(
+        self, forcefield, ensure_compatible=True, use_nagl=True, property_map={}
+    ):
         """
         Constructor.
 
@@ -145,6 +147,11 @@ def __init__(self, forcefield, ensure_compatible=True, property_map={}):
             original molecule, e.g. the original atom and residue names will be
             kept.
 
+        use_nagl : bool
+            Whether to use NAGL to compute AM1-BCC charges. If False, the default
+            is to use AmberTools via antechamber and sqm. (This option is only
+            used if NAGL is available.)
+
         property_map : dict
             A dictionary that maps system "properties" to their user defined
             values. This allows the user to refer to properties with their
@@ -158,6 +165,12 @@ def __init__(self, forcefield, ensure_compatible=True, property_map={}):
             property_map=property_map,
         )
 
+        if not isinstance(use_nagl, bool):
+            raise TypeError("'use_nagl' must be of type 'bool'")
+
+        # Set the NAGL flag.
+        self._use_nagl = use_nagl
+
         # Set the compatibility flags.
         self._tleap = False
         self._pdb2gmx = False
@@ -314,7 +327,7 @@ def run(self, molecule, work_dir=None, queue=None):
                     raise _ThirdPartyError(msg) from None
 
         # Apply AM1-BCC charges using NAGL.
-        if _has_nagl:
+        if _has_nagl and self._use_nagl:
             try:
                 _nagl.assign_partial_charges(
                     off_molecule, partial_charge_method=_nagl_model
diff --git a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py
index 07a49d24b..6e8570bb9 100644
--- a/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py
+++ b/python/BioSimSpace/Sandpit/Exscientia/Parameters/_parameters.py
@@ -463,6 +463,7 @@ def _parameterise_openff(
     forcefield,
     molecule,
     ensure_compatible=True,
+    use_nagl=True,
     work_dir=None,
     property_map={},
     **kwargs,
@@ -489,6 +490,11 @@ def _parameterise_openff(
         the parameterised molecule will preserve the topology of the original
         molecule, e.g. the original atom and residue names will be kept.
 
+    use_nagl : bool
+        Whether to use NAGL to compute AM1-BCC charges. If False, the default
+        is to use AmberTools via antechamber and sqm. (This option is only
+        used if NAGL is available.)
+
     work_dir : str
         The working directory for the process.
 
@@ -583,12 +589,21 @@ def _parameterise_openff(
         if forcefield not in _forcefields_lower:
             raise ValueError("Supported force fields are: %s" % openForceFields())
 
+    if not isinstance(ensure_compatible, bool):
+        raise TypeError("'ensure_compatible' must be of type 'bool'.")
+
+    if not isinstance(use_nagl, bool):
+        raise TypeError("'use_nagl' must be of type 'bool'.")
+
     if not isinstance(property_map, dict):
         raise TypeError("'property_map' must be of type 'dict'")
 
     # Create a default protocol.
     protocol = _Protocol.OpenForceField(
-        forcefield, ensure_compatible=ensure_compatible, property_map=property_map
+        forcefield,
+        ensure_compatible=ensure_compatible,
+        use_nagl=use_nagl,
+        property_map=property_map,
     )
 
     # Run the parameterisation protocol in the background and return
@@ -1079,7 +1094,9 @@ def _function(
 # it conforms to sensible function naming standards, i.e. "-" and "."
 # characters replaced by underscores.
 def _make_openff_function(name):
-    def _function(molecule, ensure_compatible=True, work_dir=None, property_map={}):
+    def _function(
+        molecule, ensure_compatible=True, use_nagl=True, work_dir=None, property_map={}
+    ):
         """
         Parameterise a molecule using the named force field from the
         Open Force Field initiative.
@@ -1100,6 +1117,11 @@ def _function(molecule, ensure_compatible=True, work_dir=None, property_map={}):
             molecule will preserve the topology of the original molecule, e.g.
             the original atom and residue names will be kept.
 
+        use_nagl : bool
+            Whether to use NAGL to compute AM1-BCC charges. If False, the default
+            is to use AmberTools via antechamber and sqm. (This option is only
+            used if NAGL is available.)
+
         work_dir : str
             The working directory for the process.
 
@@ -1118,6 +1140,7 @@ def _function(molecule, ensure_compatible=True, work_dir=None, property_map={}):
             name,
             molecule,
             ensure_compatible=ensure_compatible,
+            use_nagl=use_nagl,
             work_dir=work_dir,
             property_map=property_map,
         )