From 82f3c05d024b56aff19a5f9e5fc753c3b077d81c Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Sun, 8 Oct 2023 20:35:06 -0500
Subject: [PATCH 01/20] support to write out settles section for gromacs

---
 gmso/formats/top.py | 50 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index 24b83b4e6..cce585dfa 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -171,6 +171,56 @@ def write_top(top, filename, top_vars=None):
                         site.atom_type.mass.in_units(u.amu).value,
                     )
                 )
+            # Special treatment for water, may ned to consider a better way to tag rigid water
+            # Built using this https://github.com/gromacs/gromacs/blob/main/share/top/oplsaa.ff/spce.itp as reference
+            if "water" in tag.lower() and all(
+                "rigid" in site.label for site in unique_molecules[tag]["sites"]
+            ):
+                sites_list = unique_molecules[tag]["sites"]
+                water_sites = {
+                    "O": [
+                        site
+                        for site in sites_list
+                        if site.element.symbol == "O"
+                    ],
+                    "H": [
+                        site
+                        for site in sites_list
+                        if site.element.symbol == "H"
+                    ],
+                }
+
+                ow_idx = shifted_idx_map[top.get_index(water_sites["O"][0])] + 1
+                doh = np.linalg.norm(
+                    water_sites["O"][0].position.to(u.nm)
+                    - water_sites["H"][0].position.to(u.nm)
+                )
+                dhh = np.linalg.norm(
+                    water_sites["H"][0].position.to(u.nm)
+                    - water_sites["H"][1].position.to(u.nm)
+                )
+
+                # Write settles
+                out_file.write(
+                    "\n[ settles ] ;Water specific constraint algorithm\n"
+                    "; OW_idx\tfunct\tdoh\tdhh\n"
+                )
+                out_file.write(
+                    "{0:4s}{1:4s}{2:15.5f}{3:15.5f}\n".format(
+                        str(ow_idx), "1", doh, dhh
+                    )
+                )
+
+                # Write exclusion
+                out_file.write(
+                    "\n[ exclusions ] ;Exclude all interactions between water's atoms\n"
+                    "1\t2\t3\n"
+                    "2\t1\t3\n"
+                    "3\t1\t2\n"
+                )
+
+                # Skip the rest of the loop
+                continue
 
             for conn_group in [
                 "pairs",

From 904750fa75ac9c6376c31ae2e5a7b44062b12fba Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Mon, 16 Oct 2023 10:44:43 -0500
Subject: [PATCH 02/20] add isrigid to molecule

---
 gmso/abc/abstract_site.py | 8 +++++---
 gmso/formats/top.py       | 2 +-
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index 0234446ae..fa044ef5e 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -10,12 +10,14 @@
 from gmso.exceptions import GMSOError
 
 try:
-    from pydantic.v1 import Field, StrictInt, StrictStr, validator
+    from pydantic.v1 import Field, StrictBool, StrictInt, StrictStr, validator
 except ImportError:
-    from pydantic import Field, StrictInt, StrictStr, validator
+    from pydantic import Field, StrictBool, StrictInt, StrictStr, validator
 
 PositionType = Union[Sequence[float], np.ndarray, u.unyt_array]
-MoleculeType = NamedTuple("Molecule", name=StrictStr, number=StrictInt)
+MoleculeType = NamedTuple(
+    "Molecule", name=StrictStr, number=StrictInt, isrigid=StrictBool
+)
 ResidueType = NamedTuple("Residue", name=StrictStr, number=StrictInt)
 
 SiteT = TypeVar("SiteT", bound="Site")
diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index cce585dfa..7c548da6c 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -174,7 +174,7 @@ def write_top(top, filename, top_vars=None):
             # Special treatment for water, may ned to consider a better way to tag rigid water
             # Built using this https://github.com/gromacs/gromacs/blob/main/share/top/oplsaa.ff/spce.itp as reference
             if "water" in tag.lower() and all(
-                "rigid" in site.label for site in unique_molecules[tag]["sites"]
+                site.molecule.isrigid for site in unique_molecules[tag]["sites"]
             ):
                 sites_list = unique_molecules[tag]["sites"]
                 water_sites = {

From 7197b2778201ada704b0c95c3d3bd2299b3faabc Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Tue, 14 Nov 2023 16:39:04 -0600
Subject: [PATCH 03/20] add default val for moleculeType isrigid

---
 gmso/abc/abstract_site.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index fa044ef5e..5ebe49b06 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -15,9 +15,14 @@
     from pydantic import Field, StrictBool, StrictInt, StrictStr, validator
 
 PositionType = Union[Sequence[float], np.ndarray, u.unyt_array]
-MoleculeType = NamedTuple(
-    "Molecule", name=StrictStr, number=StrictInt, isrigid=StrictBool
-)
+
+
+class MoleculeType(NamedTuple):
+    name: StrictStr
+    number: StrictInt
+    isrigid: StrictBool = False
+
+
 ResidueType = NamedTuple("Residue", name=StrictStr, number=StrictInt)
 
 SiteT = TypeVar("SiteT", bound="Site")

From 19f7b717370ab48d886def394c21536fc75693e5 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Tue, 14 Nov 2023 17:30:24 -0600
Subject: [PATCH 04/20] revert change to moleculetype

---
 gmso/abc/abstract_site.py | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index 5ebe49b06..7ef1c3c22 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -16,13 +16,7 @@
 
 PositionType = Union[Sequence[float], np.ndarray, u.unyt_array]
 
-
-class MoleculeType(NamedTuple):
-    name: StrictStr
-    number: StrictInt
-    isrigid: StrictBool = False
-
-
+MoleculeType = NamedTuple("Molecule", name=StrictStr, number=StrictInt)
 ResidueType = NamedTuple("Residue", name=StrictStr, number=StrictInt)
 
 SiteT = TypeVar("SiteT", bound="Site")

From b0bb7c6b36976c7e1b3dd379f7fa2252886dd15b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 7 May 2024 15:59:17 +0000
Subject: [PATCH 05/20] [pre-commit.ci] auto fixes from pre-commit.com hooks
 for more information, see https://pre-commit.ci

---
 gmso/formats/top.py | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index e24ae574d..2734733f0 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -173,16 +173,8 @@ def write_top(top, filename, top_vars=None):
             ):
                 sites_list = unique_molecules[tag]["sites"]
                 water_sites = {
-                    "O": [
-                        site
-                        for site in sites_list
-                        if site.element.symbol == "O"
-                    ],
-                    "H": [
-                        site
-                        for site in sites_list
-                        if site.element.symbol == "H"
-                    ],
+                    "O": [site for site in sites_list if site.element.symbol == "O"],
+                    "H": [site for site in sites_list if site.element.symbol == "H"],
                 }
 
                 ow_idx = shifted_idx_map[top.get_index(water_sites["O"][0])] + 1

From a4721ce434c5812bad1075c0c3f526a9e285320f Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Mon, 13 May 2024 15:51:31 -0500
Subject: [PATCH 06/20] update molecule and residue class, fix unit tests

---
 gmso/abc/abstract_site.py         | 139 ++++++++++++++++++++++++++++--
 gmso/core/topology.py             |  20 ++++-
 gmso/external/convert_mbuild.py   |   7 +-
 gmso/formats/lammpsdata.py        |   6 +-
 gmso/formats/mol2.py              |   6 +-
 gmso/formats/top.py               |   1 +
 gmso/tests/test_convert_mbuild.py |   2 +-
 gmso/tests/test_convert_parmed.py |   4 +-
 gmso/tests/test_mol2.py           |  12 +--
 gmso/utils/sorting.py             |   4 +-
 10 files changed, 170 insertions(+), 31 deletions(-)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index b480e0b17..655237a85 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -1,14 +1,13 @@
 """Basic interaction site in GMSO that all other sites will derive from."""
 
 import warnings
-from typing import Any, ClassVar, NamedTuple, Optional, Sequence, TypeVar, Union
+from typing import Any, ClassVar, Optional, Sequence, TypeVar, Union
 
 import numpy as np
 import unyt as u
 from pydantic import (
     ConfigDict,
     Field,
-    StrictInt,
     StrictStr,
     field_serializer,
     field_validator,
@@ -21,8 +20,116 @@
 
 PositionType = Union[Sequence[float], np.ndarray, u.unyt_array]
 
-MoleculeType = NamedTuple("Molecule", name=StrictStr, number=StrictInt)
-ResidueType = NamedTuple("Residue", name=StrictStr, number=StrictInt)
+
+class Molecule(GMSOBase):
+    __iterable_attributes__: ClassVar[set] = {
+        "name",
+        "number",
+        "isrigid",
+    }
+
+    __base_doc__: ClassVar[str] = "Molecule label for interaction sites."
+
+    name_: str = Field(
+        "",
+        validate_default=True,
+        description="Name of the molecule",
+        alias="name",
+    )
+    number_: int = Field(
+        0,
+        description="The index/number of the molecule",
+        alias="number",
+    )
+    isrigid_: bool = Field(
+        False,
+        description="Indicate whether the molecule is rigid",
+    )
+    model_config = ConfigDict(
+        alias_to_fields={
+            "name": "name_",
+            "number": "number_",
+            "isrigid": "isrigid_",
+        }
+    )
+
+    @property
+    def name(self) -> str:
+        """Return the name of the molecule."""
+        return self.__dict__.get("name_")
+
+    @property
+    def number(self) -> int:
+        """Return the index/number of the moleucle."""
+        return self.__dict__.get("number_")
+
+    @property
+    def isrigid(self) -> bool:
+        """Return the rigid label of the molecule."""
+        return self.__dict__.get("isrigid_")
+
+    def __hash__(self):
+        return hash(tuple([(name, val) for name, val in self.__dict__.items()]))
+
+    def __eq__(self, other):
+        """Test if two objects are equivalent."""
+        if isinstance(other, (list, tuple)):
+            return all(
+                [val1 == val2 for val1, val2 in zip(self.__dict__.values(), other)]
+            )
+        else:
+            return self.__dict__ == other.__dict__
+
+
+class Residue(GMSOBase):
+    __iterable_attributes__: ClassVar[set] = {
+        "name",
+        "number",
+        "isrigid",
+    }
+
+    __base_doc__: ClassVar[str] = "Residue label for interaction sites."
+
+    name_: str = Field(
+        "",
+        validate_default=True,
+        description="Name of the residue",
+        alias="name",
+    )
+    number_: int = Field(
+        0,
+        description="The index/number of the residue",
+        alias="number",
+    )
+    model_config = ConfigDict(
+        alias_to_fields={
+            "name": "name_",
+            "number": "number_",
+        }
+    )
+
+    @property
+    def name(self) -> str:
+        """Return the name of the residue."""
+        return self.__dict__.get("name_")
+
+    @property
+    def number(self) -> int:
+        """Return the index/number of the residue."""
+        return self.__dict__.get("number_")
+
+    def __hash__(self):
+        return hash(tuple([(name, val) for name, val in self.__dict__.items()]))
+
+    def __eq__(self, other):
+        """Test if two objects are equivalent."""
+        if isinstance(other, (list, tuple)):
+            return all(
+                [val1 == val2 for val1, val2 in zip(self.__dict__.values(), other)]
+            )
+        else:
+            return self.__dict__ == other.__dict__
+
 
 SiteT = TypeVar("SiteT", bound="Site")
 
@@ -77,13 +184,13 @@ class Site(GMSOBase):
         alias="group",
     )
 
-    molecule_: Optional[MoleculeType] = Field(
+    molecule_: Optional[Union[Molecule, list, tuple]] = Field(
         None,
         description="Molecule label for the site, format of (molecule_name, molecule_number)",
         alias="molecule",
     )
 
-    residue_: Optional[ResidueType] = Field(
+    residue_: Optional[Union[Residue, list, tuple]] = Field(
         None,
         description="Residue label for the site, format of (residue_name, residue_number)",
         alias="residue",
@@ -127,7 +234,7 @@ def group(self) -> str:
         return self.__dict__.get("group_")
 
     @property
-    def molecule(self) -> tuple:
+    def molecule(self):
         """Return the molecule of the site."""
         return self.__dict__.get("molecule_")
 
@@ -186,12 +293,28 @@ def is_valid_position(cls, position):
         return position
 
     @field_validator("name_")
-    def inject_name(cls, value):
+    def parse_name(cls, value):
         if value == "" or value is None:
             return cls.__name__
         else:
             return value
 
+    @field_validator("residue_")
+    def parse_residue(cls, value):
+        if isinstance(value, (tuple, list)):
+            assert len(value) == 2
+            value = Residue(name=value[0], number=value[1])
+        return value
+
+    @field_validator("molecule_")
+    def parse_molecule(cls, value):
+        if isinstance(value, (tuple, list)):
+            if len(value) == 2:
+                value = Molecule(name=value[0], number=value[1])
+            elif len(value) == 3:
+                value = Molecule(name=value[0], number=value[1], isrigid=value[2])
+        return value
+
     @classmethod
     def __new__(cls, *args: Any, **kwargs: Any) -> SiteT:
         if cls is Site:
diff --git a/gmso/core/topology.py b/gmso/core/topology.py
index 856adaa7f..05a5cdd1a 100644
--- a/gmso/core/topology.py
+++ b/gmso/core/topology.py
@@ -9,7 +9,7 @@
 from boltons.setutils import IndexedSet
 
 import gmso
-from gmso.abc.abstract_site import Site
+from gmso.abc.abstract_site import Molecule, Residue, Site
 from gmso.abc.serialization_utils import unyt_to_dict
 from gmso.core.angle import Angle
 from gmso.core.angle_type import AngleType
@@ -1382,9 +1382,21 @@ def iter_sites(self, key, value):
             for site in self._sites:
                 if getattr(site, key) and getattr(site, key).name == value:
                     yield site
-        for site in self._sites:
-            if getattr(site, key) == value:
-                yield site
+        elif isinstance(value, (tuple, list)):
+            containers_dict = {"molecule": Molecule, "residue": Residue}
+            if len(value) == 2:
+                tmp = containers_dict[key](name=value[0], number=value[1])
+            else:
+                tmp = containers_dict[key](
+                    name=value[0], number=value[1], isrigid=value[2]
+                )
+            for site in self._sites:
+                if getattr(site, key) and getattr(site, key) == tmp:
+                    yield site
+        else:
+            for site in self._sites:
+                if getattr(site, key) == value:
+                    yield site
 
     def iter_sites_by_residue(self, residue_tag):
         """Iterate through this topology's sites which contain this specific residue name.
diff --git a/gmso/external/convert_mbuild.py b/gmso/external/convert_mbuild.py
index 4dfa6f03e..5ac724ce6 100644
--- a/gmso/external/convert_mbuild.py
+++ b/gmso/external/convert_mbuild.py
@@ -8,6 +8,7 @@
 from boltons.setutils import IndexedSet
 from unyt import Unit
 
+from gmso.abc.abstract_site import Residue
 from gmso.core.atom import Atom
 from gmso.core.bond import Bond
 from gmso.core.box import Box
@@ -179,12 +180,14 @@ def to_mbuild(topology, infer_hierarchy=True):
                 particle = _parse_particle(particle_map, site)
                 # Try to add the particle to a residue level
                 residue_tag = (
-                    site.residue if site.residue else ("DefaultResidue", 0)
+                    site.residue
+                    if site.residue
+                    else Residue(name="DefaultResidue", number=0)
                 )  # the 0 idx is placeholder and does nothing
                 if residue_tag in residue_dict:
                     residue_dict_particles[residue_tag] += [particle]
                 else:
-                    residue_dict[residue_tag] = mb.Compound(name=residue_tag[0])
+                    residue_dict[residue_tag] = mb.Compound(name=residue_tag.name)
                     residue_dict_particles[residue_tag] = [particle]
 
             for key, item in residue_dict.items():
diff --git a/gmso/formats/lammpsdata.py b/gmso/formats/lammpsdata.py
index 7eabc6bea..953300bb2 100644
--- a/gmso/formats/lammpsdata.py
+++ b/gmso/formats/lammpsdata.py
@@ -14,7 +14,7 @@
 from unyt.array import allclose_units
 
 import gmso
-from gmso.abc.abstract_site import MoleculeType
+from gmso.abc.abstract_site import Molecule
 from gmso.core.angle import Angle
 from gmso.core.atom import Atom
 from gmso.core.atom_type import AtomType
@@ -488,7 +488,9 @@ def _get_atoms(filename, topology, base_unyts, type_list):
             charge=charge,
             position=coord,
             atom_type=copy.deepcopy(type_list[int(atom_type) - 1]),  # 0-index
-            molecule=MoleculeType(atom_line[1], int(atom_line[1]) - 1),  # 0-index
+            molecule=Molecule(
+                name=atom_line[1], number=int(atom_line[1]) - 1
+            ),  # 0-index
         )
         element = element_by_mass(site.atom_type.mass.value)
         site.name = element.name if element else site.atom_type.name
diff --git a/gmso/formats/mol2.py b/gmso/formats/mol2.py
index 61bb2876d..91e3b5ffd 100644
--- a/gmso/formats/mol2.py
+++ b/gmso/formats/mol2.py
@@ -7,7 +7,7 @@
 import unyt as u
 
 from gmso import Atom, Bond, Box, Topology
-from gmso.abc.abstract_site import MoleculeType, ResidueType
+from gmso.abc.abstract_site import Molecule, Residue
 from gmso.core.element import element_by_name, element_by_symbol
 from gmso.formats.formats_registry import loads_as
 
@@ -151,8 +151,8 @@ def parse_ele(*symbols):
                 position=position.to("nm"),
                 element=element,
                 charge=charge,
-                residue=ResidueType(content[7], int(content[6])),
-                molecule=MoleculeType(molecule, 0),
+                residue=Residue(name=content[7], number=int(content[6])),
+                molecule=Molecule(name=molecule, number=0),
             )
             top.add_site(atom)
 
diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index 2734733f0..c3321681a 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -3,6 +3,7 @@
 import datetime
 import warnings
 
+import numpy as np
 import unyt as u
 
 from gmso.core.dihedral import Dihedral
diff --git a/gmso/tests/test_convert_mbuild.py b/gmso/tests/test_convert_mbuild.py
index a8bf2c159..f98ebce45 100644
--- a/gmso/tests/test_convert_mbuild.py
+++ b/gmso/tests/test_convert_mbuild.py
@@ -53,7 +53,7 @@ def test_from_mbuild_argon(self, ar_system):
             assert top.sites[i].name == top.sites[i].element.symbol
 
         for site in top.sites:
-            assert site.molecule[0] == "Ar"
+            assert site.molecule.name == "Ar"
 
     def test_from_mbuild_single_particle(self):
         compound = mb.Compound()
diff --git a/gmso/tests/test_convert_parmed.py b/gmso/tests/test_convert_parmed.py
index 3a702554b..eb927e29c 100644
--- a/gmso/tests/test_convert_parmed.py
+++ b/gmso/tests/test_convert_parmed.py
@@ -249,8 +249,8 @@ def test_residues_info(self, parmed_hexane_box):
         ) == len(struc.residues)
 
         for site in top_from_struc.sites:
-            assert site.residue[0] == "HEX"
-            assert site.residue[1] in list(range(0, 6))
+            assert site.residue.name == "HEX"
+            assert site.residue.number in list(range(0, 6))
 
         struc_from_top = to_parmed(top_from_struc)
         assert len(struc_from_top.residues) == len(struc.residues)
diff --git a/gmso/tests/test_mol2.py b/gmso/tests/test_mol2.py
index d7b651350..16a4f3fc5 100644
--- a/gmso/tests/test_mol2.py
+++ b/gmso/tests/test_mol2.py
@@ -63,21 +63,21 @@ def test_read_mol2(self):
 
     def test_residue(self):
         top = Topology.load(get_fn("ethanol_aa.mol2"))
-        assert np.all([site.residue[0] == "ETO" for site in top.sites])
-        assert np.all([site.residue[1] == 1 for site in top.sites])
+        assert np.all([site.residue.name == "ETO" for site in top.sites])
+        assert np.all([site.residue.number == 1 for site in top.sites])
 
         top = Topology.load(get_fn("benzene_ua.mol2"), site_type="lj")
         assert np.all(
-            [site.residue[0] == "BEN1" for site in top.iter_sites_by_residue("BEN1")]
+            [site.residue.name == "BEN1" for site in top.iter_sites_by_residue("BEN1")]
         )
         assert np.all(
-            [site.residue[1] == 1 for site in top.iter_sites_by_residue("BEN1")]
+            [site.residue.number == 1 for site in top.iter_sites_by_residue("BEN1")]
         )
         assert np.all(
-            [site.residue[0] == "BEN2" for site in top.iter_sites_by_residue("BEN2")]
+            [site.residue.name == "BEN2" for site in top.iter_sites_by_residue("BEN2")]
         )
         assert np.all(
-            [site.residue[1] == 2 for site in top.iter_sites_by_residue("BEN2")]
+            [site.residue.number == 2 for site in top.iter_sites_by_residue("BEN2")]
         )
 
     def test_lj_system(self):
diff --git a/gmso/utils/sorting.py b/gmso/utils/sorting.py
index 6382ee353..93b6d4f52 100644
--- a/gmso/utils/sorting.py
+++ b/gmso/utils/sorting.py
@@ -253,6 +253,4 @@ def reindex_molecules(top):
 
     for site in top.sites:
         mol_num = site.molecule.number
-        site.molecule = site.molecule._replace(
-            number=mol_num - offsetDict[site.molecule.name]
-        )
+        site.molecule.number = mol_num - offsetDict[site.molecule.name]

From ce0423242f8f6719aae626f73bf0ce5d4f6d9a8c Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Thu, 16 May 2024 16:55:05 -0500
Subject: [PATCH 07/20] use site.name if no element info is found

---
 gmso/formats/top.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index c3321681a..a38ddbe33 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -160,7 +160,7 @@ def write_top(top, filename, top_vars=None):
                         site.atom_type.name,
                         str(site.molecule.number + 1 if site.molecule else 1),
                         tag,
-                        site.atom_type.tags.get("element", site.element.symbol),
+                        site.atom_type.tags.get("element", site.name),
                         "1",  # TODO: care about charge groups
                         site.atom_type.charge.in_units(u.elementary_charge).value,
                         site.atom_type.mass.in_units(u.amu).value,
@@ -173,6 +173,7 @@ def write_top(top, filename, top_vars=None):
                 site.molecule.isrigid for site in unique_molecules[tag]["sites"]
             ):
                 sites_list = unique_molecules[tag]["sites"]
+
                 water_sites = {
                     "O": [site for site in sites_list if site.element.symbol == "O"],
                     "H": [site for site in sites_list if site.element.symbol == "H"],
@@ -207,9 +208,6 @@ def write_top(top, filename, top_vars=None):
                     "3\t1\t2\n"
                 )
 
-                # Skip the rest of the loop
-                continue
-
             if unique_molecules[tag]["position_restraints"]:
                 out_file.write(headers["position_restraints"])
                 for site in unique_molecules[tag]["position_restraints"]:

From d667404f9fc15239d0a31f7819891db746144ab3 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Thu, 16 May 2024 17:22:47 -0500
Subject: [PATCH 08/20] add patch for getting non-element site

---
 gmso/formats/top.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index a38ddbe33..85f5d7e7b 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -5,6 +5,7 @@
 
 import numpy as np
 import unyt as u
+from lark import UnexpectedCharacters
 
 from gmso.core.dihedral import Dihedral
 from gmso.core.element import element_by_atom_type
@@ -421,7 +422,7 @@ def _lookup_atomic_number(atom_type):
     try:
         element = element_by_atom_type(atom_type)
         return element.atomic_number
-    except GMSOError:
+    except (GMSOError, UnexpectedCharacters):
         return 0
 
 
@@ -430,7 +431,7 @@ def _lookup_element_symbol(atom_type):
     try:
         element = element_by_atom_type(atom_type)
         return element.symbol
-    except GMSOError:
+    except (GMSOError, UnexpectedCharacters):
         return "X"
 
 

From 427bf51d2633d3437be51d6fe02cd497ed6d6a74 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Mon, 20 May 2024 17:46:17 -0500
Subject: [PATCH 09/20] let element.py handle non-element issue

---
 gmso/core/element.py | 10 +++++++++-
 gmso/formats/top.py  | 28 +++++++++++++++-------------
 2 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/gmso/core/element.py b/gmso/core/element.py
index d0e93ada5..d3ab8dd84 100644
--- a/gmso/core/element.py
+++ b/gmso/core/element.py
@@ -254,6 +254,8 @@ def element_by_smarts_string(smarts_string, verbose=False):
     GMSOError
         If no matching element is found for the provided smarts string
     """
+    from lark import UnexpectedCharacters
+
     from gmso.utils.io import import_
 
     foyer = import_("foyer")
@@ -261,7 +263,13 @@ def element_by_smarts_string(smarts_string, verbose=False):
 
     PARSER = SMARTS()
 
-    symbols = PARSER.parse(smarts_string).iter_subtrees_topdown()
+    try:
+        symbols = PARSER.parse(smarts_string).iter_subtrees_topdown()
+    except UnexpectedCharacters:
+        raise GMSOError(
+            f"Failed to find an element from SMARTS string {smarts_string}. "
+            f"The SMARTS string contained unexpected characters."
+        )
 
     first_symbol = None
     for symbol in symbols:
diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index 85f5d7e7b..1b189c99a 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -5,7 +5,6 @@
 
 import numpy as np
 import unyt as u
-from lark import UnexpectedCharacters
 
 from gmso.core.dihedral import Dihedral
 from gmso.core.element import element_by_atom_type
@@ -168,6 +167,15 @@ def write_top(top, filename, top_vars=None):
                     )
                 )
 
+            if unique_molecules[tag]["position_restraints"]:
+                out_file.write(headers["position_restraints"])
+                for site in unique_molecules[tag]["position_restraints"]:
+                    out_file.write(
+                        _write_restraint(
+                            top, site, "position_restraints", shifted_idx_map
+                        )
+                    )
+
             # Special treatment for water, may ned to consider a better way to tag rigid water
             # Built using this https://github.com/gromacs/gromacs/blob/main/share/top/oplsaa.ff/spce.itp as reference
             if "water" in tag.lower() and all(
@@ -184,11 +192,11 @@ def write_top(top, filename, top_vars=None):
                 doh = np.linalg.norm(
                     water_sites["O"][0].position.to(u.nm)
                     - water_sites["H"][0].position.to(u.nm)
-                )
+                ).to_value("nm")
                 dhh = np.linalg.norm(
                     water_sites["H"][0].position.to(u.nm)
                     - water_sites["H"][1].position.to(u.nm)
-                )
+                ).to_value("nm")
 
                 # Write settles
                 out_file.write(
@@ -209,14 +217,8 @@ def write_top(top, filename, top_vars=None):
                     "3\t1\t2\n"
                 )
 
-            if unique_molecules[tag]["position_restraints"]:
-                out_file.write(headers["position_restraints"])
-                for site in unique_molecules[tag]["position_restraints"]:
-                    out_file.write(
-                        _write_restraint(
-                            top, site, "position_restraints", shifted_idx_map
-                        )
-                    )
+                # Break out of the loop, skipping connection info
+                continue
 
             for conn_group in [
                 "pairs",
@@ -422,7 +424,7 @@ def _lookup_atomic_number(atom_type):
     try:
         element = element_by_atom_type(atom_type)
         return element.atomic_number
-    except (GMSOError, UnexpectedCharacters):
+    except GMSOError:
         return 0
 
 
@@ -431,7 +433,7 @@ def _lookup_element_symbol(atom_type):
     try:
         element = element_by_atom_type(atom_type)
         return element.symbol
-    except (GMSOError, UnexpectedCharacters):
+    except GMSOError:
         return "X"
 
 

From 3f09d0893dc7c03b87f3ea4adb3fa3ff3ec4689b Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Sun, 16 Jun 2024 20:47:05 -0500
Subject: [PATCH 10/20] minor fix

---
 gmso/core/topology.py   | 3 ++-
 gmso/tests/base_test.py | 6 ++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/gmso/core/topology.py b/gmso/core/topology.py
index 05a5cdd1a..fb3862c6f 100644
--- a/gmso/core/topology.py
+++ b/gmso/core/topology.py
@@ -2,6 +2,7 @@
 
 import itertools
 import warnings
+from copy import copy
 from pathlib import Path
 
 import numpy as np
@@ -313,7 +314,7 @@ def unique_site_labels(self, label_type="molecule", name_only=False):
                 unique_tags.add(label.name if label else None)
         else:
             for site in self.sites:
-                unique_tags.add(getattr(site, label_type))
+                unique_tags.add(copy(getattr(site, label_type)))
         return unique_tags
 
     @property
diff --git a/gmso/tests/base_test.py b/gmso/tests/base_test.py
index e8f771827..884d56813 100644
--- a/gmso/tests/base_test.py
+++ b/gmso/tests/base_test.py
@@ -282,6 +282,12 @@ def typed_tip3p_rigid_system(self, water_system):
         top.identify_connections()
         ff = ForceField(get_path("tip3p-rigid.xml"))
         top = apply(top, ff)
+
+        # molecules = top.unique_site_labels(name_only=False)
+        # for molecule in molecules:
+        #     for site in top.iter_sites(key="molecule", value=molecule):
+        #         site.molecule.isrigid = True
+        #
         return top
 
     @pytest.fixture

From 927fd6c7e11d8db7d8e4fc2be575dffe1dfc3296 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Sun, 16 Jun 2024 21:50:52 -0500
Subject: [PATCH 11/20] add set_rigid method

---
 gmso/core/topology.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/gmso/core/topology.py b/gmso/core/topology.py
index fb3862c6f..40e29a46a 100644
--- a/gmso/core/topology.py
+++ b/gmso/core/topology.py
@@ -643,6 +643,18 @@ def get_scaling_factors(self, *, molecule_id=None):
             ]
         )
 
+    def set_rigid(self, molecule):
+        """Set molecule tags to rigid if they match the name or number specified.
+
+        Parameters
+        ----------
+        molecule : str, Molecule, or tuple of 2
+            Specified the molecule name and number to be set rigid.
+            If only string is provided, make all molecule of that name rigid.
+        """
+        for site in self.iter_sites(key="molecule", value=molecule):
+            site.molecule.isrigid = True
+
     def remove_site(self, site):
         """Remove a site from the topology.
 

From 3894c047449ddcf3f1eac87d20080f0343bacae3 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Sun, 16 Jun 2024 22:17:46 -0500
Subject: [PATCH 12/20] add rigid water fixture for settles tests, update mcf
 test

---
 gmso/tests/base_test.py | 18 +++++++++++++-----
 gmso/tests/test_mcf.py  |  4 ++--
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/gmso/tests/base_test.py b/gmso/tests/base_test.py
index 884d56813..772fc52c2 100644
--- a/gmso/tests/base_test.py
+++ b/gmso/tests/base_test.py
@@ -276,6 +276,15 @@ def typed_water_system(self, water_system):
         top = apply(top, ff)
         return top
 
+    @pytest.fixture
+    def typed_tip3p_system(self, water_system):
+        top = water_system
+        top.identify_connections()
+        ff = ForceField(get_path("tip3p-rigid.xml"))
+        top = apply(top, ff)
+
+        return top
+
     @pytest.fixture
     def typed_tip3p_rigid_system(self, water_system):
         top = water_system
@@ -283,11 +292,10 @@ def typed_tip3p_rigid_system(self, water_system):
         ff = ForceField(get_path("tip3p-rigid.xml"))
         top = apply(top, ff)
 
-        # molecules = top.unique_site_labels(name_only=False)
-        # for molecule in molecules:
-        #     for site in top.iter_sites(key="molecule", value=molecule):
-        #         site.molecule.isrigid = True
-        #
+        molecules = top.unique_site_labels(name_only=False)
+        for molecule in molecules:
+            top.set_rigid(molecule)
+
         return top
 
     @pytest.fixture
diff --git a/gmso/tests/test_mcf.py b/gmso/tests/test_mcf.py
index 51426be0b..036d8f3d5 100644
--- a/gmso/tests/test_mcf.py
+++ b/gmso/tests/test_mcf.py
@@ -319,8 +319,8 @@ def test_typed_ethylene(self):
 
         assert np.allclose(ff_coeffs, 2.0 * mcf_coeffs)
 
-    def test_fixed_angles(self, typed_tip3p_rigid_system):
-        top = typed_tip3p_rigid_system
+    def test_fixed_angles(self, typed_tip3p_system):
+        top = typed_tip3p_system
         write_mcf(top, "tip3p-rigid.mcf")
 
         mcf_data, mcf_idx = parse_mcf("tip3p-rigid.mcf")

From 862db26f491521b47d4d089e7c2b5d6f259bab56 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Sun, 16 Jun 2024 23:34:18 -0500
Subject: [PATCH 13/20] update test for water settles section in gromacs top

---
 gmso/formats/top.py                         |  2 +-
 gmso/tests/base_test.py                     |  5 ++-
 gmso/tests/files/settles_ref.top            | 37 +++++++++++++++++++++
 gmso/tests/files/typed_water_system_ref.top | 12 +++----
 gmso/tests/test_top.py                      | 12 +++++++
 5 files changed, 60 insertions(+), 8 deletions(-)
 create mode 100644 gmso/tests/files/settles_ref.top

diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index 1b189c99a..124fd8af3 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -286,7 +286,7 @@ def write_top(top, filename, top_vars=None):
                             )
                         if conn_group == "dihedral_restraints":
                             warnings.warn(
-                                "The diehdral_restraints writer is designed to work with"
+                                "The dihebradral_restraints writer is designed to work with"
                                 "`define = DDIHRES` clause in the GROMACS input file (.mdp)"
                             )
                             out_file.write("#endif DIHRES\n")
diff --git a/gmso/tests/base_test.py b/gmso/tests/base_test.py
index 772fc52c2..55c7b080b 100644
--- a/gmso/tests/base_test.py
+++ b/gmso/tests/base_test.py
@@ -182,6 +182,9 @@ def spce_water(self):
     def water_system(self):
         water = Topology(name="water")
         water = water.load(get_path("tip3p.mol2"))
+        for site in water.sites:
+            site.molecule.name = "WaterTIP3P"
+
         return water
 
     @pytest.fixture
@@ -289,7 +292,7 @@ def typed_tip3p_system(self, water_system):
     def typed_tip3p_rigid_system(self, water_system):
         top = water_system
         top.identify_connections()
-        ff = ForceField(get_path("tip3p-rigid.xml"))
+        ff = ForceField(get_path("tip3p.xml"))
         top = apply(top, ff)
 
         molecules = top.unique_site_labels(name_only=False)
diff --git a/gmso/tests/files/settles_ref.top b/gmso/tests/files/settles_ref.top
new file mode 100644
index 000000000..9bed22355
--- /dev/null
+++ b/gmso/tests/files/settles_ref.top
@@ -0,0 +1,37 @@
+; File tip3p written by GMSO at 2024-06-16 22:44:09.646856
+
+[ defaults ]
+; nbfunc	comb-rule	gen-pairs	fudgeLJ		fudgeQQ
+1		2		yes		0.5		0.5
+
+[ atomtypes ]
+; name	at.num		mass	charge		ptype	sigma	epsilon
+opls_111    8       16.00000    -0.83400	A        0.31506     0.63639
+opls_112    1        1.01100     0.41700	A        1.00000     0.00000
+
+[ moleculetype ]
+; name	nrexcl
+WaterTIP3P	3
+
+[ atoms ]
+; nr	type	resnr	residue		atom	cgnr	charge	mass
+1       opls_111    1       WaterTIP3P  O       1       -0.83400    16.00000
+2       opls_112    1       WaterTIP3P  H       1        0.41700     1.01100
+3       opls_112    1       WaterTIP3P  H       1        0.41700     1.01100
+
+[ settles ] ;Water specific constraint algorithm
+; OW_idx	funct	doh	dhh
+1   1           0.08925        0.15133
+
+[ exclusions ] ;Exclude all interactions between water's atoms
+1	2	3
+2	1	3
+3	1	2
+
+[ system ]
+; name
+tip3p
+
+[ molecules ]
+; molecule	nmols
+WaterTIP3P	1
diff --git a/gmso/tests/files/typed_water_system_ref.top b/gmso/tests/files/typed_water_system_ref.top
index f08e3d6c0..4b242e410 100644
--- a/gmso/tests/files/typed_water_system_ref.top
+++ b/gmso/tests/files/typed_water_system_ref.top
@@ -1,4 +1,4 @@
-; File Topology written by GMSO at 2023-04-21 15:15:49.414556
+; File tip3p written by GMSO at 2024-06-16 23:05:45.808217
 
 [ defaults ]
 ; nbfunc	comb-rule	gen-pairs	fudgeLJ		fudgeQQ
@@ -11,13 +11,13 @@ opls_112    1        1.01100     0.41700	A        1.00000     0.00000
 
 [ moleculetype ]
 ; name	nrexcl
-RES	3
+WaterTIP3P	3
 
 [ atoms ]
 ; nr	type	resnr	residue		atom	cgnr	charge	mass
-1       opls_111    1       RES         O       1       -0.83400    16.00000
-2       opls_112    1       RES         H       1        0.41700     1.01100
-3       opls_112    1       RES         H       1        0.41700     1.01100
+1       opls_111    1       WaterTIP3P  O       1       -0.83400    16.00000
+2       opls_112    1       WaterTIP3P  H       1        0.41700     1.01100
+3       opls_112    1       WaterTIP3P  H       1        0.41700     1.01100
 
 [ bonds ]
 ; ai	aj	funct	b0		kb
@@ -34,4 +34,4 @@ tip3p
 
 [ molecules ]
 ; molecule	nmols
-RES	1
+WaterTIP3P	1
diff --git a/gmso/tests/test_top.py b/gmso/tests/test_top.py
index aabcffcb9..2cdd312d2 100644
--- a/gmso/tests/test_top.py
+++ b/gmso/tests/test_top.py
@@ -149,6 +149,18 @@ def test_custom_defaults(self, typed_ethane):
         assert struct.defaults.fudgeLJ == 0.5
         assert struct.defaults.fudgeQQ == 0.5
 
+    def test_settles(self, typed_tip3p_rigid_system):
+        typed_tip3p_rigid_system.save("settles.top", overwrite=True)
+
+        with open("settles.top", "r") as f1:
+            current = f1.readlines()
+
+        with open(get_path("settles_ref.top"), "r") as f2:
+            ref = f2.readlines()
+
+        for line, ref_line in zip(current[1:], ref[1:]):
+            assert line, ref_line
+
     def test_benzene_restraints(self, typed_benzene_ua_system):
         top = typed_benzene_ua_system
 

From d861811d9cd643f1515fef86a4daa3b77809ed89 Mon Sep 17 00:00:00 2001
From: Co Quach <43968221+daico007@users.noreply.github.com>
Date: Sun, 16 Jun 2024 23:37:09 -0500
Subject: [PATCH 14/20] Update gmso/abc/abstract_site.py

Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>
---
 gmso/abc/abstract_site.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index 655237a85..bc3577dd3 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -22,6 +22,8 @@
 
 
 class Molecule(GMSOBase):
+    def __repr__(self):
+        return f"Molecule(name={self.name}, residue={self.residue}, isrigid={self.isrigid}"
     __iterable_attributes__: ClassVar[set] = {
         "name",
         "number",

From 92cba15fd07ebbeaf27bcdc963c304f3b73fbca8 Mon Sep 17 00:00:00 2001
From: Co Quach <43968221+daico007@users.noreply.github.com>
Date: Sun, 16 Jun 2024 23:37:14 -0500
Subject: [PATCH 15/20] Update gmso/abc/abstract_site.py

Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>
---
 gmso/abc/abstract_site.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index bc3577dd3..259980a33 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -84,6 +84,8 @@ def __eq__(self, other):
 
 
 class Residue(GMSOBase):
+    def __repr__(self):
+        return f"Residue(name={self.name}, residue={self.residue}"
     __iterable_attributes__: ClassVar[set] = {
         "name",
         "number",

From 07b6067ccdf229fa40cbb8d15994c2f775606809 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 17 Jun 2024 04:37:15 +0000
Subject: [PATCH 16/20] [pre-commit.ci] auto fixes from pre-commit.com hooks
 for more information, see https://pre-commit.ci

---
 gmso/abc/abstract_site.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index 259980a33..6a1d8a94b 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -23,7 +23,10 @@
 
 class Molecule(GMSOBase):
     def __repr__(self):
-        return f"Molecule(name={self.name}, residue={self.residue}, isrigid={self.isrigid}"
+        return (
+            f"Molecule(name={self.name}, residue={self.residue}, isrigid={self.isrigid}"
+        )
+
     __iterable_attributes__: ClassVar[set] = {
         "name",
         "number",

From dddb59e82aaeacaf3649b452e5d218f4570e180b Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Sun, 16 Jun 2024 23:38:14 -0500
Subject: [PATCH 17/20] remove isrigid for residue

---
 gmso/abc/abstract_site.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index 655237a85..b68b35405 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -85,7 +85,6 @@ class Residue(GMSOBase):
     __iterable_attributes__: ClassVar[set] = {
         "name",
         "number",
-        "isrigid",
     }
 
     __base_doc__: ClassVar[str] = "Residue label for interaction sites."

From 86b83a620c95ba895c265433236460c2605eb35d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 17 Jun 2024 04:38:26 +0000
Subject: [PATCH 18/20] [pre-commit.ci] auto fixes from pre-commit.com hooks
 for more information, see https://pre-commit.ci

---
 gmso/abc/abstract_site.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gmso/abc/abstract_site.py b/gmso/abc/abstract_site.py
index ae1c6401f..399a2b6dc 100644
--- a/gmso/abc/abstract_site.py
+++ b/gmso/abc/abstract_site.py
@@ -89,6 +89,7 @@ def __eq__(self, other):
 class Residue(GMSOBase):
     def __repr__(self):
         return f"Residue(name={self.name}, residue={self.residue}"
+
     __iterable_attributes__: ClassVar[set] = {
         "name",
         "number",

From 4ac478cd6205310506aeef1bb06c583f0ff22526 Mon Sep 17 00:00:00 2001
From: Co Quach <daico007@gmail.com>
Date: Sun, 16 Jun 2024 23:45:55 -0500
Subject: [PATCH 19/20] add more check when setting molecule/residue

---
 gmso/core/topology.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/gmso/core/topology.py b/gmso/core/topology.py
index 40e29a46a..54580f7c7 100644
--- a/gmso/core/topology.py
+++ b/gmso/core/topology.py
@@ -1399,10 +1399,19 @@ def iter_sites(self, key, value):
             containers_dict = {"molecule": Molecule, "residue": Residue}
             if len(value) == 2:
                 tmp = containers_dict[key](name=value[0], number=value[1])
-            else:
+            elif len(value) == 3:
                 tmp = containers_dict[key](
                     name=value[0], number=value[1], isrigid=value[2]
                 )
+            else:
+                raise ValueError(
+                    f"""
+                        Argument value was passed as {value},
+                        but should be an indexible iterable of
+                        [name, number, isrigid] where name is type string,
+                        number is type int, and isrigid is type bool.
+                    """
+                )
             for site in self._sites:
                 if getattr(site, key) and getattr(site, key) == tmp:
                     yield site

From bde8b6d8eacf1ce842d6c9cdf4b1201946ae1f7e Mon Sep 17 00:00:00 2001
From: Co Quach <43968221+daico007@users.noreply.github.com>
Date: Mon, 17 Jun 2024 12:41:41 -0500
Subject: [PATCH 20/20] Update gmso/formats/top.py

Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>
---
 gmso/formats/top.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gmso/formats/top.py b/gmso/formats/top.py
index 124fd8af3..bfe4644f5 100644
--- a/gmso/formats/top.py
+++ b/gmso/formats/top.py
@@ -286,7 +286,7 @@ def write_top(top, filename, top_vars=None):
                             )
                         if conn_group == "dihedral_restraints":
                             warnings.warn(
-                                "The dihebradral_restraints writer is designed to work with"
+                                "The dihedral_restraints writer is designed to work with"
                                 "`define = DDIHRES` clause in the GROMACS input file (.mdp)"
                             )
                             out_file.write("#endif DIHRES\n")