Persistent Conformer Generation Issue in psiresp.Molecule.from_rdkit()

[n-kristovskiy]

Dear Lily Wang,

I'm developing a molecule parameterization protocol using psiresp and have encountered a persistent issue with conformer generation when using Molecule.from_rdkit().

Problem Description
After initially using the minimize='mmff94' flag in Molecule.from_rdkit(), the conformer generation now consistently produces only 1 conformer regardless of specified parameters. This behavior persists despite:

Removing all conformers after molecule creation (RESP_mol.conformers.clear())

1. Reverting minimize to None
2. Trying different environments
3. Various parameter combinations
4. Complete Reproduction Code

Complete Reproduction Code

trimers_smi = {'GKcrG': '[H]N([H])C([H])([H])C(=O)N([H])[C@@]([H])(C(=O)N([H])C([H])([H])C([H])=O)C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)C(\\[H])=C(/[H])C([H])([H])[H]'}
trimers_chem = {'GKcrG': Chem.MolFromSmiles(trimers_smi, sanitize)}
constraint_dict = {
    'GKcrG': {
        'symmetric_list': [],
        'charge_atom_dict': {4:-0.34790, 26:0.27470, 5:-0.24000, 6:0.73410, 7:-0.58940, 27:0.14260},
        'charge_of_monomer': 0.0000,
    }
}

param_mol_name = 'GKcrG'
psiresp_dict = {}

# Problematic molecule creation
RESP_mol = psiresp.Molecule.from_rdkit(
    trimers_chem[param_mol_name],
    optimize_geometry=True,
    charge=0,
    conformer_generation_options={
        'n_conformer_pool': 10000,
        'n_max_conformers': 10,
        'energy_window': 150,
        'keep_original_conformer': False,
        'minimize': 'mmff94'  # Initially caused the issue
    }
)

# Attempted solutions that didn't work:
# RESP_mol.conformers.clear()
# minimize=None in conformer_generation_options

psiresp_dict[param_mol_name] = RESP_mol

# Constraints setup (works normally)
constraints = psiresp.ChargeConstraintOptions(symmetric_atoms_are_equivalent=False)
constraints = pt.add_constraint(
    RESP_mol,
    constraint_dict[param_mol_name]['symmetric_list'],
    constraint_dict[param_mol_name]['charge_atom_dict'],
    constraint_dict[param_mol_name]['charge_of_monomer'],
    constraints=constraints
)

# Execution
folder_name = 'psiresp_data/'
path_folder = f'{folder_name}/{str(*psiresp_dict.keys())}'
name_of_system = pt.get_unique_folder_name(path_folder)
print(f'The psiresp data will be recorded at: {name_of_system}')
pt.show_list_of_conf(f'{name_of_system}/optimization/', True) 
# checks the number of files in the optimization folder with the msgpack extension.

Observed Behavior

Output always shows only 1 conformer being generated:

generate-conformers: 100%|██████████| 1/1 [00:00<00:00, 12710.01it/s]
SystemExit: Exiting to allow running QM computations; commands are in .../run_optimization.sh
Number of conformers: 1

Key Observations

1. Works normally with Molecule.from_smiles()
2. Requires from_rdkit() due to stereochemistry handling
3. Problem persists even after:

• Environment recreation
• Removing all conformers
• Resetting minimization options

Could this be related to some internal state being preserved? Any insight would be greatly appreciated.

Best regards,
Nick

[lilyminium]

Thanks for the thorough report, Nick -- I can't look at this immediately but I'll try to get to it over the weekend. Just to help me out in reproduction and diagnosis, could you please add the package versions in the environment you're using? (e.g. with conda list or pip list)

[n-kristovskiy]

Update on a problem with conformer generation.

When initializing molecules using psiresp.Molecule.from_rdkit() with
minimize=None (before that I already specified minimize='mmff94'). Subsequent execution of job.run() does not generate conformers.

I tried using explicit conformers clear (RESP_mol.conformers.clear()) before executing job.run(). (I.e. Molecule(name=C9H20, charge=0) with 1 conformers turns into Molecule(name=C9H20, charge=0) with 0 conformers). Then the subsequent execution of job.run() allows to get the given number of conformers.

However, the conformer generation shows an anomalous behavior:

The first conformer is always flat (2D structure), regardless of the keep_original_conformer parameter. This started to happen only after changing minimization settings and clearing conformers

I looked at the conformer structures before the minimize problem occurred, there every conformer was 3D and optimized.

I tried to remove information about flat conformer:

def del_2d_conformer(job, name_of_system):
    # Remove the conformer file
 hash_name = job.molecules[0].conformers[0].qcmol.get_hash()
 file_name = next(glob.iglob(f'{name_of_system}/optimization/*{hash_name}*'), None)
 print(file_name)
 if file_name:
 os. remove(file_name)
 else:
 print("File not found")
 # Edit sh file
 sh_file_path = f'{name_of_system}/optimization/run_optimization. sh'
 with open(sh_file_path, 'r') as f:
 lines = f.readlines()
 filtered_lines = [line for line in lines if hash_name not in line]
 with open(sh_file_path, 'w') as f:
 f. writelines(filtered_lines)
 # Delete conformer in job
 del job.molecules[0].conformers[0]
 return job

But at further calculation of partial charges it leads to appearance of negative protons.

Yaml of my envairoment:

name: topmol4
channels:
  - psi4
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - acpype=2022.7.21=pyhd8ed1ab_1
  - alembic=1.9.1=pyhd8ed1ab_0
  - alsa-lib=1.2.8=h166bdaf_0
  - ambit=0.6=py38h53dec33_2
  - anyio=3.6.2=pyhd8ed1ab_0
  - appdirs=1.4.4=pyh9f0ad1d_0
  - argon2-cffi=21.3.0=pyhd8ed1ab_0
  - argon2-cffi-bindings=21.2.0=py38h0a891b7_3
  - arpack=3.7.0=hdefa2d7_2
  - arrow-cpp=11.0.0=ha770c72_5_cpu
  - asttokens=2.2.1=pyhd8ed1ab_0
  - attr=2.5.1=h166bdaf_1
  - attrs=22.2.0=pyh71513ae_0
  - autoconf=2.71=pl5321h2b4cb7a_1
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  - aws-c-cal=0.5.20=hc60faf5_6
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  - aws-c-compression=0.2.16=h034cb4b_3
  - aws-c-event-stream=0.2.18=h75388cd_6
  - aws-c-http=0.7.4=hf084cc8_2
  - aws-c-io=0.13.17=h10df833_2
  - aws-c-mqtt=0.8.6=hc41645a_6
  - aws-c-s3=0.2.4=h1b8f470_3
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  - gstreamer=1.14.1=h5eee18b_1
  - gstreamer-orc=0.4.33=h166bdaf_0
  - h5py=3.1.0=nompi_py38hafa665b_100
  - hdf4=4.2.15=h9772cbc_5
  - hdf5=1.10.6=nompi_h3c11f04_101
  - icu=73.2=h59595ed_0
  - idna=3.4=pyhd8ed1ab_0
  - importlib-metadata=6.0.0=pyha770c72_0
  - importlib_metadata=6.0.0=hd8ed1ab_0
  - importlib_resources=5.10.2=pyhd8ed1ab_0
  - iniconfig=2.0.0=pyhd8ed1ab_0
  - intel-openmp=2021.4.0=h06a4308_3561
  - ipykernel=6.20.1=pyh210e3f2_0
  - ipython=8.8.0=pyh41d4057_0
  - ipython_genutils=0.2.0=py_1
  - ipywidgets=7.7.2=pyhd8ed1ab_0
  - isodate=0.7.2=pyhd8ed1ab_0
  - jack=1.9.21=h583fa2b_2
  - jedi=0.18.2=pyhd8ed1ab_0
  - jinja2=3.1.2=pyhd8ed1ab_1
  - joblib=1.2.0=pyhd8ed1ab_0
  - jpeg=9e=h166bdaf_2
  - jsonschema=4.17.3=pyhd8ed1ab_0
  - jupyter_client=7.4.8=pyhd8ed1ab_0
  - jupyter_core=5.1.3=py38h578d9bd_0
  - jupyter_events=0.6.3=pyhd8ed1ab_0
  - jupyter_server=2.5.0=pyhd8ed1ab_0
  - jupyter_server_terminals=0.4.4=pyhd8ed1ab_1
  - jupyterlab_pygments=0.2.2=pyhd8ed1ab_0
  - jupyterlab_widgets=1.1.4=pyhd8ed1ab_0
  - kernel-headers_linux-64=2.6.32=he073ed8_15
  - keyutils=1.6.1=h166bdaf_0
  - kiwisolver=1.4.4=py38h43d8883_1
  - krb5=1.20.1=h81ceb04_0
  - lame=3.100=h166bdaf_1003
  - lcms2=2.14=hfd0df8a_1
  - ld_impl_linux-64=2.39=hcc3a1bd_1
  - lerc=4.0.0=h27087fc_0
  - libabseil=20220623.0=cxx17_h05df665_6
  - libaec=1.0.6=h9c3ff4c_0
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  - libarrow=11.0.0=h2ebd325_5_cpu
  - libblas=3.9.0=12_linux64_mkl
  - libbrotlicommon=1.0.9=h166bdaf_8
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  - libbrotlienc=1.0.9=h166bdaf_8
  - libcap=2.66=ha37c62d_0
  - libcblas=3.9.0=12_linux64_mkl
  - libclang=14.0.6=default_h7634d5b_1
  - libclang13=14.0.6=default_h9986a30_1
  - libcrc32c=1.1.2=h9c3ff4c_0
  - libcups=2.3.3=h36d4200_3
  - libcurl=8.11.1=hc9e6f67_0
  - libdb=6.2.32=h9c3ff4c_0
  - libdeflate=1.14=h166bdaf_0
  - libecpint=1.0.7=hfebba4c_0
  - libedit=3.1.20221030=h5eee18b_0
  - libev=4.33=h516909a_1
  - libevent=2.1.10=h28343ad_4
  - libexpat=2.6.4=h5888daf_0
  - libffi=3.4.2=h7f98852_5
  - libflac=1.4.2=h27087fc_0
  - libgcc=14.2.0=h77fa898_1
  - libgcc-devel_linux-64=12.2.0=h3b97bd3_19
  - libgcc-ng=14.2.0=h69a702a_1
  - libgcrypt=1.10.1=h166bdaf_0
  - libgfortran-ng=7.5.0=h14aa051_20
  - libgfortran4=7.5.0=h14aa051_20
  - libgfortran5=14.2.0=hd5240d6_1
  - libglib=2.80.2=hf974151_0
  - libgomp=14.2.0=h77fa898_1
  - libgoogle-cloud=2.7.0=h21dfe5b_1
  - libgpg-error=1.46=h620e276_0
  - libgrpc=1.51.1=h4fad500_1
  - libiconv=1.17=h166bdaf_0
  - libint2=2.7.1=h2fe1556_15
  - libjpeg-turbo=2.1.4=h166bdaf_0
  - liblapack=3.9.0=12_linux64_mkl
  - libllvm14=14.0.6=hcd5def8_4
  - libllvm15=15.0.7=h5cf9203_3
  - libmamba=1.5.0=h658169a_0
  - libmambapy=1.5.0=py38he0d8f90_0
  - libnetcdf=4.8.1=nompi_hcd642e3_100
  - libnghttp2=1.58.0=h47da74e_1
  - libnsl=2.0.0=h7f98852_0
  - libogg=1.3.4=h7f98852_1
  - libopenblas=0.3.21=pthreads_h78a6416_3
  - libopus=1.3.1=h7f98852_1
  - libpng=1.6.39=h753d276_0
  - libpq=12.20=hdbd6064_0
  - libprotobuf=3.21.12=h3eb15da_0
  - libsanitizer=12.2.0=h46fd767_19
  - libsndfile=1.1.0=hcb278e6_1
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  - nspr=4.35=h27087fc_0
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  - openssl=3.4.1=h7b32b05_0
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  - packaging=22.0=pyhd8ed1ab_0
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  - pkgutil-resolve-name=1.3.10=pyhd8ed1ab_0
  - platformdirs=2.6.2=pyhd8ed1ab_0
  - plotly=5.9.0=py38h06a4308_0
  - pluggy=1.0.0=pyhd8ed1ab_5
  - ply=3.11=py_1
  - pooch=1.6.0=pyhd8ed1ab_0
  - postgresql=12.20=hbf900ed_0
  - prometheus_client=0.16.0=pyhd8ed1ab_0
  - prompt-toolkit=3.0.36=pyha770c72_0
  - psi4=1.6.1+5b9f6e3=py38h1bd450f_0
  - psiresp=0.4.2=pyhd8ed1ab_0
  - psiresp-base=0.4.2=pyhd8ed1ab_0
  - psutil=5.9.4=py38h0a891b7_0
  - psycopg2=2.9.9=py38h5eee18b_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - ptyprocess=0.7.0=pyhd3deb0d_0
  - pubchempy=1.0.4=py_0
  - pulseaudio=16.1=h126f2b6_0
  - pure_eval=0.2.2=pyhd8ed1ab_0
  - py-cpuinfo=9.0.0=pyhd8ed1ab_0
  - py3dmol=2.1.0=pyhd8ed1ab_0
  - pyarrow=11.0.0=py38hf05218d_5_cpu
  - pybel=0.13.2=py_0
  - pybind11-abi=4=hd8ed1ab_3
  - pycairo=1.23.0=py38h190342e_0
  - pycosat=0.6.4=py38h0a891b7_1
  - pycparser=2.21=pyhd8ed1ab_0
  - pydantic=1.10.4=py38h1de0b5d_1
  - pyedr=0.7.1=pyhd8ed1ab_0
  - pygments=2.14.0=pyhd8ed1ab_0
  - pyopenssl=24.2.1=pyhd8ed1ab_2
  - pyparsing=3.0.9=pyhd8ed1ab_0
  - pyqt=5.15.4=py38hfa26641_0
  - pyqt5-sip=12.9.0=py38hfa26641_0
  - pyrsistent=0.19.3=py38h1de0b5d_0
  - pysocks=1.7.1=pyha2e5f31_6
  - pytest=7.2.0=pyhd8ed1ab_2
  - python=3.8.16=he550d4f_1_cpython
  - python-dateutil=2.8.2=pyhd8ed1ab_0
  - python-fastjsonschema=2.16.2=pyhd8ed1ab_0
  - python-json-logger=2.0.7=pyhd8ed1ab_0
  - python_abi=3.8=3_cp38
  - pytng=0.3.0=py38hcf6129a_0
  - pytz=2022.7=pyhd8ed1ab_0
  - pyyaml=6.0=py38h0a891b7_5
  - pyzmq=24.0.1=py38hfc09fa9_1
  - qcelemental=0.25.1=pyhd8ed1ab_1
  - qcengine=0.24.1=pyhd8ed1ab_0
  - qcfractal=0.15.8.1=py38h578d9bd_0
  - qcfractal-core=0.15.8.1=py38h578d9bd_0
  - qt-main=5.15.2=h53bd1ea_10
  - rdkit=2023.03.3=py38h36d2b2f_0
  - re2=2023.02.01=hcb278e6_0
  - readline=8.1.2=h0f457ee_0
  - reportlab=3.6.12=py38h8786f81_2
  - reproc=14.2.4=h0b41bf4_0
  - reproc-cpp=14.2.4=hcb278e6_0
  - requests=2.28.1=pyhd8ed1ab_1
  - requests-file=2.0.0=pyhd8ed1ab_0
  - requests-toolbelt=1.0.0=pyhd8ed1ab_0
  - rfc3339-validator=0.1.4=pyhd8ed1ab_0
  - rfc3986-validator=0.1.1=pyh9f0ad1d_0
  - rhash=1.4.3=h166bdaf_0
  - ruamel.yaml=0.17.21=py38h0a891b7_2
  - ruamel.yaml.clib=0.2.7=py38h1de0b5d_1
  - s2n=1.3.37=h3358134_0
  - scikit-learn=1.2.0=py38h1e1a916_0
  - scipy=1.10.0=py38h10c12cc_0
  - seaborn=0.12.2=hd8ed1ab_0
  - seaborn-base=0.12.2=pyhd8ed1ab_0
  - send2trash=1.8.0=pyhd8ed1ab_0
  - setuptools=65.6.3=pyhd8ed1ab_0
  - simint=0.7=h642920c_1
  - sip=6.5.1=py38h709712a_2
  - six=1.16.0=pyh6c4a22f_0
  - snappy=1.1.9=hbd366e4_2
  - sniffio=1.3.0=pyhd8ed1ab_0
  - soupsieve=2.3.2.post1=pyhd8ed1ab_0
  - sqlalchemy=1.3.24=py38h0a891b7_1
  - sqlite=3.45.3=h5eee18b_0
  - stack_data=0.6.2=pyhd8ed1ab_0
  - statsmodels=0.13.5=py38h26c90d9_2
  - sysroot_linux-64=2.12=he073ed8_15
  - tenacity=8.1.0=pyhd8ed1ab_0
  - terminado=0.17.1=pyh41d4057_0
  - threadpoolctl=3.1.0=pyh8a188c0_0
  - tidynamics=1.0.0=py_0
  - tinycss2=1.2.1=pyhd8ed1ab_0
  - tk=8.6.12=h27826a3_0
  - toml=0.10.2=pyhd8ed1ab_0
  - tomli=2.0.1=pyhd8ed1ab_0
  - toolz=0.12.0=pyhd8ed1ab_0
  - tornado=6.2=py38h0a891b7_1
  - tqdm=4.64.1=pyhd8ed1ab_0
  - traitlets=5.8.0=pyhd8ed1ab_0
  - tree=2.2.1=hb9d3cd8_0
  - typing-extensions=4.4.0=hd8ed1ab_0
  - typing_extensions=4.4.0=pyha770c72_0
  - tzcode=2022g=h166bdaf_0
  - tzdata=2022g=h191b570_0
  - unicodedata2=15.0.0=py38h0a891b7_0
  - urllib3=1.26.13=pyhd8ed1ab_0
  - wcwidth=0.2.5=pyh9f0ad1d_2
  - webencodings=0.5.1=py_1
  - websocket-client=1.5.1=pyhd8ed1ab_0
  - wheel=0.38.4=pyhd8ed1ab_0
  - widgetsnbextension=3.6.4=pyhd8ed1ab_0
  - wrapt=1.15.0=py38h1de0b5d_0
  - xcb-util=0.4.1=hb711507_2
  - xcb-util-image=0.4.0=hb711507_2
  - xcb-util-keysyms=0.4.1=hb711507_0
  - xcb-util-renderutil=0.3.10=hb711507_0
  - xcb-util-wm=0.4.2=hb711507_0
  - xkeyboard-config=2.38=h0b41bf4_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.7.2=h7f98852_0
  - xorg-libxau=1.0.12=hb9d3cd8_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h7f98852_1
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-libxt=1.2.1=h7f98852_2
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h7f98852_1002
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - yaml-cpp=0.7.0=h27087fc_2
  - zeep=4.3.1=pyhff2d567_0
  - zeromq=4.3.4=h9c3ff4c_1
  - zipp=3.11.0=pyhd8ed1ab_0
  - zlib=1.2.13=h166bdaf_4
  - zstandard=0.19.0=py38h5945529_1
  - zstd=1.5.2=h6239696_4
  - pip:
      - amberlite==16.0
      - ambertools==17.0
      - libchebipy==1.0.10
      - mmpbsa-py==16.0
      - packmol-memgen==1.0.5rc0
      - parmed==3.2.0
      - pdb4amber==1.7.dev0
      - pytraj==2.0.5
      - sander==16.0