Unable to make OFFMol from RDMol: RDMol has unspecified stereochemistry

[suice07]

Hello everyone,

I am creating Molecule object from a rdkit mol,with a conformer file,ligand.mol2 and a protein file 5x1a.pdb, after merging it to a complex file 5x1a_complex.pdb, it is impossible to generate Molecule object in this way.

smi` = 'CC1=NN(c2ccc(C)c(C)c2)C(=O)/C1=N\\Nc1cccc(-c2cccc(C(=O)O)c2)c1O'
rdkit_mol = Chem.MolFromPDBFile('test04192/5x1a_complex.pdb')
rdkit_mol_split = Chem.rdmolops.SplitMolByPDBResidues(rdkit_mol)
ligand = rdkit_mol_split['UNL']
ligand = Chem.RemoveHs(ligand)
reference_mol = Chem.MolFromSmiles(smi)
prepared_ligand = AllChem.AssignBondOrdersFromTemplate(reference_mol, ligand)
prepared_ligand.AddConformer(ligand.GetConformer(0))
prepared_ligand = Chem.rdmolops.AddHs(prepared_ligand, addCoords=True)
off_mol = Molecule.from_rdkit(rdkit_mol)


Traceback (most recent call last):
  File "test2.py", line 18, in <module>
    off_mol = Molecule.from_rdkit(rdkit_mol)
  File "/root/miniconda3/lib/python3.7/site-packages/openff/toolkit/utils/base_wrapper.py", line 51, in wrapped_function
    value = func(*args, **kwargs)
  File "/root/miniconda3/lib/python3.7/site-packages/openff/toolkit/topology/molecule.py", line 5004, in from_rdkit
    _cls=cls,
  File "/root/miniconda3/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 1462, in from_rdkit
    err_msg_prefix="Unable to make OFFMol from RDMol: ",
  File "/root/miniconda3/lib/python3.7/site-packages/openff/toolkit/utils/rdkit_wrapper.py", line 2323, in _detect_undefined_stereo
    raise UndefinedStereochemistryError(msg)
openff.toolkit.utils.exceptions.UndefinedStereochemistryError: Unable to make OFFMol from RDMol: Unable to make OFFMol from RDMol: RDMol has unspecified stereochemistry. RDMol name: DIHYDROPYRIMIDINASE-RELATED PROTEIN 2Undefined chiral centers are:
 - Atom C (index 3794)
 - Atom C (index 3795)
 - Atom C (index 3796)
 - Atom C (index 3801)
 - Atom C (index 3804)
 - Atom C (index 3806)
 - Atom C (index 3809)
 - Atom C (index 3813)
 - Atom C (index 3814)
 - Atom C (index 3816)
 - Atom C (index 3820)
Bonds with undefined stereochemistry are:
 - Bond 23 (atoms 24-22 of element (N-C)
 - Bond 390 (atoms 386-384 of element (N-C)
 - Bond 481 (atoms 475-473 of element (N-C)
 - Bond 860 (atoms 844-842 of element (N-C)
 - Bond 1273 (atoms 1246-1244 of element (N-C)
 - Bond 1409 (atoms 1380-1378 of element (N-C)
 - Bond 1576 (atoms 1546-1544 of element (N-C)
 - Bond 1695 (atoms 1663-1661 of element (N-C)
 - Bond 1782 (atoms 1749-1747 of element (N-C)
 - Bond 2007 (atoms 1972-1970 of element (N-C)
 - Bond 2717 (atoms 2663-2661 of element (N-C)
 - Bond 3005 (atoms 2945-2943 of element (N-C)
 - Bond 3029 (atoms 2969-2967 of element (N-C)
 - Bond 3343 (atoms 3277-3275 of element (N-C)
 - Bond 3537 (atoms 3469-3467 of element (N-C)
 - Bond 3577 (atoms 3507-3505 of element (N-C)
 - Bond 3674 (atoms 3599-3597 of element (N-C)
 - Bond 3707 (atoms 3632-3630 of element (N-C)
 - Bond 3724 (atoms 3649-3647 of element (N-C)
 - Bond 3765 (atoms 3690-3688 of element (N-C)
 - Bond 3795 (atoms 3719-3717 of element (N-C)

Here is the error. I am having the openff-toolkit==0.10.7,how could I generate the Molecule object correctly.

[Yoshanuikabundi]

Hiya! The problem is most likely that your molecule has undefined stereochemistry - it's difficult to be more specific without seeing the PDB you're loading. The OpenFF Toolkit requires all molecules to have fully defined stereochemistry to reduce errors - we've made a virtue of being very strict about what we can put in a Molecule. Just having coordinates that specify stereochemistry isn't enough, it actually needs to be defined on the molecular graph.

You can try inferring stereochemistry from the PDB coordinates, or you can create a Molecule without stereochemistry at the risk of missing out on force field parameters that specify stereochemistry with off_mol = Molecule.from_rdkit(rdkit_mol, allow_undefined_stereo=True)

[suice07]

Hiya! The problem is most likely that your molecule has undefined stereochemistry - it's difficult to be more specific without seeing the PDB you're loading. The OpenFF Toolkit requires all molecules to have fully defined stereochemistry to reduce errors - we've made a virtue of being very strict about what we can put in a Molecule. Just having coordinates that specify stereochemistry isn't enough, it actually needs to be defined on the molecular graph.

You can try inferring stereochemistry from the PDB coordinates, or you can create a Molecule without stereochemistry at the risk of missing out on force field parameters that specify stereochemistry with off_mol = Molecule.from_rdkit(rdkit_mol, allow_undefined_stereo=True)

Thanks so much for the quick reply, I think from PDBfile, some bond information is missing, so I tried to generate ff using another way,but come with this error,is this still means the stereochemistry information is missing so that no tool can be used to generate forcefield?or it is because the ligand is name is unknown acid, so it is not able to generate forcefield?

File "/root/miniconda3/lib/python3.7/site-packages/openff/toolkit/utils/toolkit_registry.py", line 380, in call
    raise ValueError(msg)
ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name 'TEST' and SMILES '[C][C]1=[N][N]([c]2[c][c][c]([C])[c]([C])[c]2)[C](=[O])/[C]1=[N]\[N-][c]1[c][c][c][c](-[c]2[c][c][c][c]([C](=[O])[O-])[c]2)[c]1[O-]', 'partial_charge_method': 'am1bcc', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around The RDKit version 2022.09.5, ToolkitWrapper around AmberTools version 21.0, ToolkitWrapper around Built-in Toolkit version None]
 ToolkitWrapper around The RDKit version 2022.09.5 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1bcc' is not available from RDKitToolkitWrapper. Available charge methods are ['mmff94']
 ToolkitWrapper around AmberTools version 21.0 <class 'subprocess.CalledProcessError'> : Command '['antechamber', '-i', 'molecule.sdf', '-fi', 'sdf', '-o', 'charged.mol2', '-fo', 'mol2', '-pf', 'yes', '-dr', 'n', '-c', 'bcc', '-nc', '-3.0']' returned non-zero exit status 1.
 ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1bcc"" is not supported by the Built-in toolkit. Available charge methods are ['zeros', 'formal_charge']

[Yoshanuikabundi]

It looks like you've successfully got the molecule into the Toolkit but AmberTools doesn't like it for some reason. Could you provide the output of conda list in the environment where you got that error, and also all the code you ran and input files you used to get that error?

[suice07]

It looks like you've successfully got the molecule into the Toolkit but AmberTools doesn't like it for some reason. Could you provide the output of conda list in the environment where you got that error, and also all the code you ran and input files you used to get that error?

_libgcc_mutex             0.1                 conda_forge    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       1_gnu    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
absl-py                   1.0.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
acemd3                    3.4.1                cuda1111_0    acellera
aiohttp                   3.8.1            py39hb9d737c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
aiosignal                 1.2.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
alsa-lib                  1.2.3                h516909a_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ambertools                21.12            py39hc630cb1_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
amberutils                21.0                     pypi_0    pypi
anaconda-client           1.11.0             pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
argon2-cffi-bindings      21.2.0           py39h3811e60_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
arpack                    3.7.0                hdefa2d7_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
astor                     0.8.1              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
asttokens                 2.0.5              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
async-timeout             4.0.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
autograd                  1.5                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
autograd-gamma            0.5.0              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
backports                 1.0                        py_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
beautifulsoup4            4.10.0             pyha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bel-resources             0.0.3                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
biopython                 1.79             py39h3811e60_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
blinker                   1.4                        py_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
blosc                     1.21.0               h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
boost                     1.74.0           py39h5472131_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
boost-cpp                 1.74.0               h6cacc03_7    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
brotli                    1.0.9                h7f98852_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
brotli-bin                1.0.9                h7f98852_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
brotlipy                  0.7.0           py39h3811e60_1003    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bzip2                     1.0.8                h7f98852_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
c-ares                    1.18.1               h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ca-certificates           2023.01.10           h06a4308_0
cached-property           1.5.2                hd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cached_property           1.5.2              pyha770c72_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cachetools                5.0.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cairo                     1.16.0            ha12eb4b_1010    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi                   2022.12.7        py39h06a4308_0
cffi                      1.15.0           py39h4bc2ebd_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cftime                    1.6.0            py39hd257fcd_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cirpy                     1.0.2                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
click-plugins             1.1.1                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cloudpickle               2.0.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
clyent                    1.2.2                      py_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
comm                      0.1.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda-package-handling    2.0.2              pyh38be061_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda-package-streaming   0.7.0              pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
configargparse            1.5.3              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cryptography              36.0.2           py39hd97740a_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cudatoolkit               11.1.1              h6406543_10    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
curl                      7.82.0               h7bff187_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cython                    0.29.28          py39h5a03fae_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
dbus                      1.13.6               h5008d03_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
debugpy                   1.5.1            py39he80948d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
deeppurpose               0.0.5              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
deeptime                  0.4.4            py39h2ad29b5_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
dgl                       0.8.1                    py39_0    dglteam
dgllife                   0.2.9              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
dill                      0.3.6              pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
docutils                  0.16             py39hf3d152e_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
entrypoints               0.4                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
et_xmlfile                1.1.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
executing                 0.8.3              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
expat                     2.4.8                h27087fc_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fftw                      3.3.10          nompi_h77c792f_102    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig                2.13.96              h8e229c2_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fonts-conda-ecosystem     1                             0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fonts-conda-forge         1                             0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fonttools                 4.31.2           py39hb9d737c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
formulaic                 0.5.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
freetype                  2.10.4               h0708190_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
frozenlist                1.3.0            py39hb9d737c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
future                    0.18.2           py39hf3d152e_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fuzzywuzzy                0.18.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gawk                      5.1.0                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gettext                   0.19.8.1          h73d1719_1008    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
giflib                    5.2.1                h36c2ea0_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
google-auth               2.6.5              pyh6c4a22f_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
google-auth-oauthlib      0.4.6              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
graphlib-backport         1.0.3              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
greenlet                  1.1.2            py39he80948d_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
griddataformats           0.7.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
grpcio                    1.45.0           py39h0f497a6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gsd                       2.5.1            py39hce5d2b2_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gsl                       2.7                  he838d99_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gst-plugins-base          1.20.1               hcf0ee16_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gstreamer                 1.20.1               hd4edc92_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gym                       0.21.0           py39hef51801_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
h5py                      3.7.0           nompi_py39h63b1161_100    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
hdf4                      4.2.15               h10796ff_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
hdf5                      1.12.1          nompi_h2386368_104    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
htmd                      2.0.5                    py39_0    acellera
htmd-deps                 2.0.5                    py39_0    acellera
hyperopt                  0.2.5              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
icu                       69.1                 h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
idna                      3.3                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
importlib-metadata        4.11.3           py39hf3d152e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
importlib_resources       5.6.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
interface_meta            1.3.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ipykernel                 6.20.2             pyh210e3f2_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ipython                   8.2.0            py39hf3d152e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ipython_genutils          0.2.0                      py_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ipywidgets                7.7.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jbig                      2.1               h7f98852_2003    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jedi                      0.18.1           py39hf3d152e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jinja2                    3.1.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jobqueues                 0.8.7                    py39_0    acellera
jpeg                      9e                   h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jsonschema                4.4.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jupyter                   1.0.0            py39hf3d152e_7    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jupyter_client            7.2.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jupyter_console           6.4.3              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jupyter_core              4.9.2            py39hf3d152e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jupyterlab_widgets        1.1.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
keyutils                  1.6.1                h166bdaf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
kiwisolver                1.4.2            py39hf939315_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
krb5                      1.19.3               h3790be6_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lcms2                     2.12                 hddcbb42_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lerc                      3.0                  h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libblas                   3.9.0           13_linux64_openblas    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libbrotlicommon           1.0.9                h7f98852_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libbrotlidec              1.0.9                h7f98852_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libbrotlienc              1.0.9                h7f98852_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcblas                  3.9.0           13_linux64_openblas    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libclang                  13.0.1          default_hc23dcda_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcurl                   7.82.0               h7bff187_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libdeflate                1.10                 h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libedit                   3.1.20191231         he28a2e2_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libev                     4.33                 h516909a_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libevent                  2.1.10               h9b69904_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libffi                    3.4.2                h7f98852_5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng                 12.2.0              h65d4601_19    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng            11.2.0              h69a702a_14    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran5              11.2.0              h5c6108e_14    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libglib                   2.70.2               h174f98d_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp                   12.2.0              h65d4601_19    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv                  1.16                 h516909a_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
liblapack                 3.9.0           13_linux64_openblas    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libllvm13                 13.0.1               hf817b99_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnetcdf                 4.8.1           nompi_hb3fd0d9_101    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnghttp2                1.47.0               h727a467_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnsl                    2.0.0                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libogg                    1.3.4                h7f98852_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libopus                   1.3.1                h7f98852_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng                    1.6.37               h21135ba_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpq                     14.2                 hd57d9b9_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libprotobuf               3.20.2               h6239696_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libsodium                 1.0.18               h36c2ea0_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libssh2                   1.10.0               ha56f1ee_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libtiff                   4.3.0                h542a066_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid                   2.32.1            h7f98852_1000    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libwebp                   1.2.2                h3452ae3_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libwebp-base              1.2.2                h7f98852_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxcb                    1.13              h7f98852_1004    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2                   2.9.12               h885dcf4_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxslt                   1.1.33               h0ef7038_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libzip                    1.8.0                h4de3113_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libzlib                   1.2.13               h166bdaf_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lifelines                 0.27.4             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lxml                      4.8.0            py39hb9d737c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lzo                       2.10              h516909a_1000    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
markdown                  3.3.6              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
markupsafe                2.1.1            py39hb9d737c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
matplotlib                3.5.1            py39hf3d152e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
matplotlib-base           3.5.1            py39h2fa2bec_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mdanalysis                2.1.0            py39h5a03fae_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mdtraj                    1.9.7            py39h138c130_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mistune                   0.8.4           py39h3811e60_1005    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mmcif_pdbx                2.0.0              pyh44b312d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mmtf-python               1.1.2                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
moleculekit               1.6.1            py39h3fd9d12_0    acellera
mpi                       1.0                     openmpi    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mpi4py                    3.1.3            py39h5418507_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mrcfile                   1.3.0              pyh44b312d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
msgpack-python            1.0.3            py39hf939315_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
multidict                 6.0.2            py39hb9d737c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
multiprocess              0.70.14          py39hb9d737c_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
multisplitby              0.0.1                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mysql-common              8.0.28               haf5c9bc_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mysql-libs                8.0.28               h28c427c_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
natsort                   8.2.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nbclient                  0.5.13           py39h06a4308_0
nbconvert                 6.5.4            py39h06a4308_0
nbformat                  5.2.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ncurses                   6.3                  h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nest-asyncio              1.5.4              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
netcdf-fortran            4.5.4           nompi_h2b6e579_100    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
netcdf4                   1.5.8           nompi_py39h64b754b_101    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
networkx                  2.7.1              pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nglview                   3.0.3              pyh8a188c0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ninja                     1.11.1               h924138e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nomkl                     1.0                  h5ca1d4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
notebook                  6.4.10             pyha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nspr                      4.32                 h9c3ff4c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nss                       3.77                 h2350873_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
numexpr                   2.8.3           py39hf625f34_101    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
numpy                     1.22.3           py39h18676bf_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
oauthlib                  3.2.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ocl-icd                   2.3.1                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ocl-icd-system            1.0.0                         1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openbabel                 3.1.1            py39hee2736e_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openff-forcefields        2.0.0              pyh6c4a22f_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openff-toolkit            0.10.3             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openff-toolkit-base       0.10.3             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openjpeg                  2.4.0                hb52868f_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openmm                    7.7.0            py39h0b75dae_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openmmforcefields         0.10.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openmpi                   4.1.3              h846660c_103    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openpyxl                  3.1.1            py39h72bdee0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl                   1.1.1t               h7f8727e_0
packaging                 21.3               pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
packmol                   20.010               h86c2bf4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
packmol-memgen            1.2.1rc0                 pypi_0    pypi
pandas                    1.4.1            py39hde0f152_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pandas-flavor             0.2.0                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pandoc                    2.17.1.1             ha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
parmed                    3.4.3            py39he80948d_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
parso                     0.8.3              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pathos                    0.3.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
patsy                     0.5.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pcre                      8.45                 h9c3ff4c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pdb2pqr                   3.6.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pdbfixer                  1.8.1              pyh6c4a22f_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
perl                      5.32.1          2_h7f98852_perl5    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pickleshare               0.7.5                   py_1003    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pillow                    9.0.1            py39hae2aec6_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pint                      0.20.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pip                       22.0.4             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pixman                    0.40.0               h36c2ea0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
plotly                    5.13.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
plumed                    2.7.3           nompi_h8de8e23_100    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
plumed2                   2.3.3+htmd.4                  4    acellera
pox                       0.3.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ppft                      1.7.6.6            pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
prettytable               3.5.0            py39h06a4308_0
prody                     2.0.2            py39h5a03fae_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
prometheus_client         0.13.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
prompt-toolkit            3.0.27             pyha770c72_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
prompt_toolkit            3.0.27               hd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
propka                    3.5.0            py39hcca971b_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
protobuf                  3.20.2           py39h5a03fae_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
protocolinterface         0.4.5                      py_0    acellera
psfgen                    1.6.9                         0    acellera
psutil                    5.9.0            py39h3811e60_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pthread-stubs             0.4               h36c2ea0_1001    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ptvsd                     4.3.2            py39hb9d737c_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
py3dmol                   1.8.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyasn1                    0.4.8                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pyasn1-modules            0.2.7                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pybel                     0.13.2                     py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
pycairo                   1.21.0           py39h0934665_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pycparser                 2.21               pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyemma                    2.5.12           py39h4661b88_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyjwt                     2.3.0              pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pymongo                   4.1.1            py39h5a03fae_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pypdb                     2.0                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyqt                      5.12.3           py39hf3d152e_8    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyqt-impl                 5.12.3           py39hde8b62d_8    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyqt5-sip                 4.19.18          py39he80948d_8    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyqtchart                 5.12             py39h0fcd23e_8    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyqtwebengine             5.12.1           py39h0fcd23e_8    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyrsistent                0.18.1           py39h3811e60_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pysocks                   1.7.1            py39hf3d152e_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytables                  3.7.0            py39h2669a42_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytdc                     0.3.6              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python                    3.9.12          h9a8a25e_1_cpython    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-levenshtein        0.12.2           py39hb9d737c_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-wget               3.2                        py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi                3.9                      2_cp39    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytorch                   1.12.1          cpu_py39h9dbd814_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
pytorch-lightning         0.8.5                      py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2022.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyu2f                     0.1.5              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyyaml                    6.0              py39hb9d737c_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyzmq                     22.3.0           py39h37b5a0c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
qt                        5.12.9               h1304e3e_6    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
qtconsole                 5.3.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
qtconsole-base            5.3.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
qtpy                      2.1.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ratelimit                 2.2.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ray                       2.3.1                h105e827_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
rdkit                     2022.03.1        py39h89e00b9_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
readline                  8.1                  h46c0cb4_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
regex                     2022.3.15        py39hb9d737c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
reportlab                 3.5.68           py39he59360d_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
requests                  2.27.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
requests-file             1.5.1              pyh9f0ad1d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
requests-oauthlib         1.3.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
rsa                       4.8                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sander                    16.0                     pypi_0    pypi
scikit-learn              1.0.2            py39h4dfa638_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
scipy                     1.8.0            py39hee8e79c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
seaborn                   0.11.2               hd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
seaborn-base              0.11.2             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools                59.5.0           py39hf3d152e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
six                       1.16.0             pyh6c4a22f_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
smirnoff99frosst          1.1.0              pyh44b312d_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
snappy                    1.1.8                he1b5a44_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
soupsieve                 2.3.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sqlalchemy                1.4.33           py39hb9d737c_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sqlite                    3.37.1               h4ff8645_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
stack_data                0.2.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
statsmodels               0.13.2           py39hce5d2b2_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tenacity                  8.2.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tensorboard               2.8.0              pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tensorboard-data-server   0.6.0            py39hd97740a_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tensorboard-plugin-wit    1.8.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tensorboardx              2.5                pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
terminado                 0.13.3           py39hf3d152e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
testpath                  0.6.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tinycss2                  1.2.1            py39h06a4308_0
tinydb                    4.7.0              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tk                        8.6.12               h27826a3_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
torch-scatter             2.0.9            py39h3225a05_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tornado                   6.1              py39h3811e60_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tqdm                      4.63.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
trimesh                   3.12.0             pyh6c4a22f_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
typing-extensions         4.2.0                hd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
typing_extensions         4.2.0              pyha770c72_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tzdata                    2022a                h191b570_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ucx                       1.12.1               ha20872e_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
unicodedata2              14.0.0           py39h3811e60_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
vina                      1.1.101                       0    acellera
wcwidth                   0.2.5              pyh9f0ad1d_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
webencodings              0.5.1                      py_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
werkzeug                  2.1.1              pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
widgetsnbextension        3.6.0            py39hf3d152e_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
wrapt                     1.14.1           py39hb9d737c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xarray                    2023.2.0           pyhd8ed1ab_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xdrfile                   1.1.4                h7f98852_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xlrd                      2.0.1              pyhd8ed1ab_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xmltodict                 0.12.0                     py_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
xorg-kbproto              1.0.7             h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libice               1.0.10               h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libx11               1.7.2                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxau               1.0.9                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxext              1.3.4                h7f98852_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxt                1.2.1                h7f98852_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-xproto               7.0.31            h7f98852_1007    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz                        5.2.5                h516909a_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
yaml                      0.2.5                h7f98852_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
yarl                      1.7.2            py39hb9d737c_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zeromq                    4.3.4                h9c3ff4c_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zlib                      1.2.13               h166bdaf_4    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zstandard                 0.19.0           py39h29414ee_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
zstd                      1.5.2                ha95c52a_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

here is the conda list output, I am refering to this link

from openff.toolkit.topology import Molecule, Topology
from rdkit import Chem
from rdkit.Chem import AllChem
import openmm.app as app
from openmm import unit,Platform
import mdtraj as md
import pdbfixer
import numpy as np
from openmmforcefields.generators import GAFFTemplateGenerator


def prepare_protein(pdbfile,ignore_missing_residues=True, 
                        ignore_terminal_missing_residues=True, 
                        ph=7.0):
        """
        Use pdbfixer to prepare the protein from a PDB file. Hetero atoms such as ligands are
        removed and non-standard residues replaced. Missing atoms to existing residues are added.
        Missing residues are ignored by default, but can be included.

        Parameters
        ----------
        pdb_file: pathlib.Path or str
            PDB file containing the system to simulate.
        ignore_missing_residues: bool, optional
            If missing residues should be ignored or built.
        ignore_terminal_missing_residues: bool, optional
            If missing residues at the beginning and the end of a chain should be ignored or built.
        ph: float, optional
            pH value used to determine protonation state of residues

        Returns
        -------
        fixer: pdbfixer.pdbfixer.PDBFixer
            Prepared protein system.
        """
        fixer = pdbfixer.PDBFixer(pdbfile)
        fixer.removeHeterogens()  # co-crystallized ligands are unknown to PDBFixer
        fixer.findMissingResidues()  # identify missing residues, needed for identification of missing atoms

        # if missing terminal residues shall be ignored, remove them from the dictionary
        if ignore_terminal_missing_residues:
            chains = list(fixer.topology.chains())
            keys = fixer.missingResidues.keys()
            for key in list(keys):
                chain = chains[key[0]]
                if key[1] == 0 or key[1] == len(list(chain.residues())):
                    del fixer.missingResidues[key]

        # if all missing residues shall be ignored ignored, clear the dictionary
        if ignore_missing_residues:
            fixer.missingResidues = {}

        fixer.findNonstandardResidues()  # find non-standard residue
        fixer.replaceNonstandardResidues()  # replace non-standard residues with standard one
        fixer.findMissingAtoms()  # find missing heavy atoms
        fixer.addMissingAtoms()  # add missing atoms and residues
        fixer.addMissingHydrogens(ph)  # add missing hydrogens
        return fixer
pdbfile = 'test04192/5x1a.pdb'
smi = 'CC1=NN(c2ccc(C)c(C)c2)C(=O)/C1=N\\Nc1cccc(-c2cccc(C(=O)O)c2)c1O'
ligand = Chem.MolFromMol2File('test04192/ligand_clean.mol2')
ligand = Chem.AddHs(ligand)
off_mol = Molecule.from_rdkit(ligand)
off_mol.name = 'UNL'
element_counter_dict = {}
for off_atom, rdkit_atom in zip(off_mol.atoms, ligand.GetAtoms()):
    element = rdkit_atom.GetSymbol()
    if element in element_counter_dict.keys():
        element_counter_dict[element] += 1
    else:
        element_counter_dict[element] = 1
        off_atom.name = element + str(element_counter_dict[element])
off_mol_topology = off_mol.to_topology()
mol_topology = off_mol_topology.to_openmm()
mol_positions = off_mol.conformers[0]
mol_positions_nm = unit.Quantity(mol_positions.value_in_unit(unit.nanometers), unit.nanometers)
omm_mol = app.Modeller(mol_topology, mol_positions_nm)
protein = prepare_protein(pdbfile)
md_protein_topology = md.Topology.from_openmm(protein.topology)  # using mdtraj for protein top
md_ligand_topology = md.Topology.from_openmm(omm_mol.topology)  # using mdtraj for ligand top
md_complex_topology = md_protein_topology.join(md_ligand_topology)  # add them together
complex_topology = md_complex_topology.to_openmm()
total_atoms = len(protein.positions) + len(omm_mol.positions)
complex_positions = unit.Quantity(np.zeros([total_atoms, 3]), unit=unit.nanometers)
complex_positions[: len(protein.positions)] = protein.positions  # add protein positions
complex_positions[len(protein.positions) :] = omm_mol.positions  # add ligand positions

forcefield = app.ForceField('amber14-all.xml','amber14/tip3pfb.xml')
if ligand is not None:
        gaff = GAFFTemplateGenerator(
        molecules=Molecule.from_rdkit(ligand)
        )
        forcefield.registerTemplateGenerator(gaff.generator)

modeller = app.Modeller(complex_topology, complex_positions)
modeller.addSolvent(forcefield, padding=1.0 * unit.nanometers, ionicStrength=0.15 * unit.molar)

below is the mol2 file I load in the code in text form

@<TRIPOS>MOLECULE
TEST
 33 36 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1 N          64.6250   41.8100  -29.6810 N.pl3   1  UNL1       -0.1137
      2 N          64.2020   42.7600  -28.7510 N.2     1  UNL1       -0.1528
      3 C          64.4910   44.0110  -28.9750 C.2     1  UNL1        0.1707
      4 C          64.1890   45.1870  -28.2020 C.2     1  UNL1        0.1009
      5 C          65.2330   44.4850  -30.1440 C.2     1  UNL1        0.2922
      6 C          63.4360   45.1650  -26.9130 C.3     1  UNL1        0.0556
      7 N          64.6540   46.2470  -28.7700 N.2     1  UNL1       -0.1739
      8 N          65.3160   45.9130  -29.9790 N.am    1  UNL1       -0.1539
      9 O          65.6880   43.7840  -31.0770 O.2     1  UNL1       -0.2661
     10 C          65.9540   46.7820  -30.8890 C.ar    1  UNL1        0.0768
     11 C          65.2290   47.5060  -31.8040 C.ar    1  UNL1        0.0165
     12 C          65.8320   48.3650  -32.7090 C.ar    1  UNL1       -0.0032
     13 C          67.2020   48.5050  -32.6980 C.ar    1  UNL1       -0.0257
     14 C          67.8430   49.4300  -33.6740 C.3     1  UNL1        0.0307
     15 C          67.9330   47.7860  -31.7880 C.ar    1  UNL1       -0.0245
     16 C          69.4300   47.9550  -31.7930 C.3     1  UNL1        0.0307
     17 C          67.3190   46.9320  -30.8900 C.ar    1  UNL1        0.0123
     18 C          63.6760   40.8990  -30.2480 C.ar    1  UNL1        0.1302
     19 C          63.3690   40.9930  -31.6090 C.ar    1  UNL1        0.0215
     20 C          62.4640   40.1300  -32.1620 C.ar    1  UNL1        0.0016
     21 C          61.8510   39.1660  -31.4010 C.ar    1  UNL1        0.0033
     22 C          62.1320   39.0430  -30.0450 C.ar    1  UNL1        0.0403
     23 C          63.0450   39.9190  -29.5000 C.ar    1  UNL1        0.2124
     24 O          63.3880   39.8630  -28.1340 O.3     1  UNL1       -0.2851
     25 C          61.4920   38.0260  -29.2220 C.ar    1  UNL1        0.0033
     26 C          62.2590   37.2910  -28.3220 C.ar    1  UNL1        0.0001
     27 C          61.6850   36.3120  -27.5150 C.ar    1  UNL1        0.0002
     28 C          60.3350   36.0510  -27.5910 C.ar    1  UNL1        0.0066
     29 C          59.5580   36.7730  -28.4830 C.ar    1  UNL1        0.0798
     30 C          60.1480   37.7360  -29.2720 C.ar    1  UNL1        0.0067
     31 C          58.1320   36.5410  -28.6040 C.2     1  UNL1        0.3878
     32 O          57.6980   36.1020  -29.7120 O.co2   1  UNL1       -0.2406
     33 O          57.2920   36.7990  -27.5370 O.co2   1  UNL1       -0.2406
@<TRIPOS>BOND
     1     1    18    1
     2     1     2    1
     3     2     3    2
     4     3     5    1
     5     3     4    1
     6     4     7    2
     7     4     6    1
     8     5     9    2
     9     5     8   am
    10     7     8    1
    11     8    10    1
    12    10    11   ar
    13    10    17   ar
    14    11    12   ar
    15    12    13   ar
    16    13    14    1
    17    13    15   ar
    18    15    16    1
    19    15    17   ar
    20    18    19   ar
    21    18    23   ar
    22    19    20   ar
    23    20    21   ar
    24    21    22   ar
    25    22    23   ar
    26    22    25    1
    27    23    24    1
    28    25    30   ar
    29    25    26   ar
    30    26    27   ar
    31    27    28   ar
    32    28    29   ar
    33    29    30   ar
    34    29    31    1
    35    31    32   ar
    36    31    33   ar

I have no idea about how to fix that,now . Maybe I am having too many transformations so it is hard for the toolkit to continue the job?

[mattwthompson]

Something is wrong with how RDKit parses that file and/or how the RDKit molecule is prepared. If all you need is the molecule loaded up from SMILES anyway, the toolkit offers a more direct way of handling that in addition to many other pathways.

I can assign partial charges from that SMILES pattern without issue using the most recent version of OpenFF tools and dependencies, although it takes a while since AM1 is slow.

from openff.toolkit import Molecule

molecule = Molecule.from_smiles("CC1=NN(c2ccc(C)c(C)c2)C(=O)/C1=N\\Nc1cccc(-c2cccc(C(=O)O)c2)c1O")
molecule.assign_partial_charges(partial_charge_method="am1bcc")

Note also that you're using an old version (0.10.3) of the toolkit which won't be supported for much longer. Newer versions include a plethora of bugfixes useful features, such as loading PDB files directly.