Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Failing to assign AM1 charges with ambertools on macOS-13 #1947

Open
lilyminium opened this issue Oct 21, 2024 · 0 comments
Open

Failing to assign AM1 charges with ambertools on macOS-13 #1947

lilyminium opened this issue Oct 21, 2024 · 0 comments

Comments

@lilyminium
Copy link
Collaborator

lilyminium commented Oct 21, 2024 •
edited
Loading

Issue

I'm seeing a weird issue in NAGL CI where I can't seem to assign AM1 charges to methane using AmberTools on macOS-13. This test passes with macOS-latest and a related test passed with macOS-12 before I updated the CI matrix. It might be a good idea to test across a wider matrix of Mac versions.

I haven't tried with other charge methods like am1bcc as I uncovered this from a failing NAGL test.

Maybe related to #1911?

To Reproduce

The test I'm running at the moment is:

@pytest.mark.skipif(not sum([OPENEYE_AVAILABLE, AMBERTOOLS_AVAILABLE]), reason="requires a charge toolkit")
def test_can_charge_methane():
    # verify we can assign AM1 charges to methane
    # See https://github.com/openforcefield/openff-nagl/issues/152 for more

    mol = Molecule.from_smiles("C")
    mol.assign_partial_charges("am1-mulliken")

Output

E       ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '' and SMILES '[H][C]([H])([H])[H]', 'partial_charge_method': 'am1-mulliken', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
E       Available toolkits are: [ToolkitWrapper around The RDKit version 2024.03.5, ToolkitWrapper around AmberTools version 23.6, ToolkitWrapper around Built-in Toolkit version None]
E        ToolkitWrapper around The RDKit version 2024.03.5 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1-mulliken' is not available from RDKitToolkitWrapper. Available charge methods are {'mmff94': {}, 'gasteiger': {}}
E        ToolkitWrapper around AmberTools version 23.6 <class 'subprocess.CalledProcessError'> : Command '['antechamber', '-i', 'molecule.sdf', '-fi', 'sdf', '-o', 'charged.mol2', '-fo', 'mol2', '-pf', 'yes', '-dr', 'n', '-c', 'mul', '-nc', '0.0']' returned non-zero exit status 1.
E        ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1-mulliken"" is not supported by the Built-in toolkit. Available charge methods are {'zeros': {'rec_confs': 0, 'min_confs': 0, 'max_confs': 0}, 'formal_charge': {'rec_confs': 0, 'min_confs': 0, 'max_confs': 0}}
../../../micromamba/envs/openff-nagl-test/lib/python3.10/site-packages/openff/toolkit/utils/toolkit_registry.py:280: ValueError

Computing environment (please complete the following information):

  • Operating system: macOS-13
  • Output of running conda list

Notable packages:

  • ambertools 23.6 (passes in macOS-latest)
  • RDKit 2024.03.5 (I put in the !=2024.03.6 pin I found in the toolkit in case it was that; if of interest, a related test did fail with 2024.03.6 as well)
  • openff-toolkit-base 0.16.5

Full:


micromamba list
  /Users/runner/micromamba-bin/micromamba list -r /Users/runner/micromamba -n openff-nagl-test
  List of packages in environment: "/Users/runner/micromamba/envs/openff-nagl-test"
  
    Name                       Version       Build                              Channel    
  ───────────────────────────────────────────────────────────────────────────────────────────
    ambertools                 23.6          cuda_None_nompi_py310h496d21a_105  conda-forge
    arpack                     3.9.1         nompi_hf81eadf_101                 conda-forge
    blosc                      1.21.6        h7d75f6d_0                         conda-forge
    brotli                     1.1.0         h00291cd_2                         conda-forge
    brotli-bin                 1.1.0         h00291cd_2                         conda-forge
    brotli-python              1.1.0         py310h53e7c6a_2                    conda-forge
    bson                       0.5.9         py_0                               conda-forge
    bzip2                      1.0.8         hfdf4475_7                         conda-forge
    c-ares                     1.34.2        h32b1619_0                         conda-forge
    ca-certificates            2024.8.30     h8857fd0_0                         conda-forge
    cached-property            1.5.2         hd8ed1ab_1                         conda-forge
    cached_property            1.5.2         pyha770c72_1                       conda-forge
    cachetools                 5.5.0         pyhd8ed1ab_0                       conda-forge
    cairo                      1.18.0        h37bd5c4_3                         conda-forge
    certifi                    2024.8.30     pyhd8ed1ab_0                       conda-forge
    cffi                       1.17.1        py310hfce808e_0                    conda-forge
    chardet                    5.2.0         py310h2ec42d9_2                    conda-forge
    charset-normalizer         3.4.0         pyhd8ed1ab_0                       conda-forge
    click                      8.1.7         unix_pyh707e725_0                  conda-forge
    click-option-group         0.5.6         pyhd8ed1ab_0                       conda-forge
    cloudpickle                3.1.0         pyhd8ed1ab_1                       conda-forge
    codecov                    2.1.13        pyhd8ed1ab_0                       conda-forge
    colorama                   0.4.6         pyhd8ed1ab_0                       conda-forge
    contourpy                  1.3.0         py310hfa8da69_2                    conda-forge
    coverage                   7.6.3         py310h72eadd2_1                    conda-forge
    cpython                    3.10.15       py310hd8ed1ab_2                    conda-forge
    cycler                     0.12.1        pyhd8ed1ab_0                       conda-forge
    cytoolz                    1.0.0         py310h837254d_1                    conda-forge
    dask-core                  2024.10.0     pyhd8ed1ab_0                       conda-forge
    dask-jobqueue              0.9.0         pyhd8ed1ab_0                       conda-forge
    distributed                2024.10.0     pyhd8ed1ab_0                       conda-forge
    exceptiongroup             1.2.2         pyhd8ed1ab_0                       conda-forge
    execnet                    2.1.1         pyhd8ed1ab_0                       conda-forge
    expat                      2.6.3         hac325c4_0                         conda-forge
    fftw                       3.3.10        nompi_h292e606_110                 conda-forge
    filelock                   3.16.1        pyhd8ed1ab_0                       conda-forge
    font-ttf-dejavu-sans-mono  2.37          hab24e00_0                         conda-forge
    font-ttf-inconsolata       3.000         h77eed37_0                         conda-forge
    font-ttf-source-code-pro   2.038         h77eed37_0                         conda-forge
    font-ttf-ubuntu            0.83          h77eed37_3                         conda-forge
    fontconfig                 2.14.2        h5bb23bf_0                         conda-forge
    fonts-conda-ecosystem      1             0                                  conda-forge
    fonts-conda-forge          1             0                                  conda-forge
    fonttools                  4.54.1        py310h837254d_0                    conda-forge
    freetype                   2.12.1        h60636b9_2                         conda-forge
    freetype-py                2.3.0         pyhd8ed1ab_0                       conda-forge
    fsspec                     2024.9.0      pyhff2d567_0                       conda-forge
    gmp                        6.3.0         hf036a51_2                         conda-forge
    gmpy2                      2.1.5         py310hade44e5_2                    conda-forge
    greenlet                   3.1.1         py310h53e7c6a_0                    conda-forge
    h2                         4.1.0         pyhd8ed1ab_0                       conda-forge
    hdf4                       4.2.15        h8138101_7                         conda-forge
    hdf5                       1.14.4        nompi_h57e3b00_101                 conda-forge
    hpack                      4.0.0         pyh9f0ad1d_0                       conda-forge
    hyperframe                 6.0.1         pyhd8ed1ab_0                       conda-forge
    icu                        75.1          h120a0e1_0                         conda-forge
    idna                       3.10          pyhd8ed1ab_0                       conda-forge
    importlib-metadata         8.5.0         pyha770c72_0                       conda-forge
    importlib_metadata         8.5.0         hd8ed1ab_0                         conda-forge
    importlib_resources        6.4.5         pyhd8ed1ab_0                       conda-forge
    iniconfig                  2.0.0         pyhd8ed1ab_0                       conda-forge
    jinja2                     3.1.4         pyhd8ed1ab_0                       conda-forge
    joblib                     1.4.2         pyhd8ed1ab_0                       conda-forge
    kiwisolver                 1.4.7         py310hfa8da69_0                    conda-forge
    krb5                       1.21.3        h37d8d59_0                         conda-forge
    lcms2                      2.16          ha2f27b4_0                         conda-forge
    lerc                       4.0.0         hb486fe8_0                         conda-forge
    libabseil                  20240722.0    cxx17_hac325c4_1                   conda-forge
    libaec                     1.1.3         h73e2aa4_0                         conda-forge
    libblas                    3.9.0         22_osx64_openblas                  conda-forge
    libboost                   1.84.0        hbe88bda_6                         conda-forge
    libboost-python            1.84.0        py310h767a3e0_6                    conda-forge
    libbrotlicommon            1.1.0         h00291cd_2                         conda-forge
    libbrotlidec               1.1.0         h00291cd_2                         conda-forge
    libbrotlienc               1.1.0         h00291cd_2                         conda-forge
    libcblas                   3.9.0         22_osx64_openblas                  conda-forge
    libcurl                    8.10.1        h58e7537_0                         conda-forge
    libcxx                     19.1.2        hf95d169_0                         conda-forge
    libdeflate                 1.22          h00291cd_0                         conda-forge
    libedit                    3.1.20191231  h0678c8f_2                         conda-forge
    libev                      4.33          h10d778d_2                         conda-forge
    libexpat                   2.6.3         hac325c4_0                         conda-forge
    libffi                     3.4.2         h0d85af4_5                         conda-forge
    libgfortran                5.0.0         13_2_0_h97931a8_3                  conda-forge
    libgfortran5               13.2.0        h2873a65_3                         conda-forge
    libglib                    2.82.2        hb6ef654_0                         conda-forge
    libhwloc                   2.11.1        default_h456cccd_1000              conda-forge
    libiconv                   1.17          hd75f5a5_2                         conda-forge
    libintl                    0.22.5        hdfe23c8_3                         conda-forge
    libjpeg-turbo              3.0.0         h0dc2134_1                         conda-forge
    liblapack                  3.9.0         22_osx64_openblas                  conda-forge
    libnetcdf                  4.9.2         nompi_h976d569_115                 conda-forge
    libnghttp2                 1.58.0        h64cf6d3_1                         conda-forge
    libopenblas                0.3.27        openmp_h8869122_1                  conda-forge
    libpng                     1.6.44        h4b8f8c9_0                         conda-forge
    libpq                      16.4          h365486b_3                         conda-forge
    libprotobuf                5.27.5        h62b0dff_2                         conda-forge
    librdkit                   2024.03.5     hbc19afa_3                         conda-forge
    libsqlite                  3.46.1        h4b8f8c9_0                         conda-forge
    libssh2                    1.11.0        hd019ec5_0                         conda-forge
    libtiff                    4.7.0         h583c2ba_1                         conda-forge
    libtorch                   2.4.1         cpu_mkl_hdb27336_102               conda-forge
    libuv                      1.49.2        hd79239c_0                         conda-forge
    libwebp-base               1.4.0         h10d778d_0                         conda-forge
    libxcb                     1.17.0        hf1f96e2_0                         conda-forge
    libxml2                    2.12.7        heaf3512_4                         conda-forge
    libzip                     1.11.1        h3116616_0                         conda-forge
    libzlib                    1.3.1         hd23fc13_2                         conda-forge
    lightning-utilities        0.11.8        pyhd8ed1ab_0                       conda-forge
    llvm-openmp                19.1.2        hf78d878_0                         conda-forge
    locket                     1.0.0         pyhd8ed1ab_0                       conda-forge
    lz4-c                      1.9.4         hf0c8a7f_0                         conda-forge
    markupsafe                 3.0.2         py310h72eadd2_0                    conda-forge
    matplotlib-base            3.9.2         py310h449bdf7_1                    conda-forge
    mkl                        2023.2.0      h54c2260_50500                     conda-forge
    mpc                        1.3.1         h9d8efa1_1                         conda-forge
    mpfr                       4.2.1         haed47dc_3                         conda-forge
    mpmath                     1.3.0         pyhd8ed1ab_0                       conda-forge
    msgpack-python             1.1.0         py310hfa8da69_0                    conda-forge
    munkres                    1.1.4         pyh9f0ad1d_0                       conda-forge
    ncurses                    6.5           hf036a51_1                         conda-forge
    netcdf-fortran             4.6.1         nompi_h4dd9276_107                 conda-forge
    networkx                   3.4.1         pyhd8ed1ab_0                       conda-forge
    numpy                      1.26.4        py310h4bfa8fc_0                    conda-forge
    openff-amber-ff-ports      0.0.4         pyhca7485f_0                       conda-forge
    openff-forcefields         2024.09.0     pyhff2d567_0                       conda-forge
    openff-interchange-base    0.3.29        pyhd8ed1ab_0                       conda-forge
    openff-models              0.1.2         pyhca7485f_0                       conda-forge
    openff-recharge            0.5.2         pyhd8ed1ab_0                       conda-forge
    openff-toolkit-base        0.16.5        pyhd8ed1ab_0                       conda-forge
    openff-units               0.2.2         pyhca7485f_0                       conda-forge
    openff-utilities           0.1.12        pyhd8ed1ab_0                       conda-forge
    openjpeg                   2.5.2         h7310d3a_0                         conda-forge
    openssl                    3.3.2         hd23fc13_0                         conda-forge
    packaging                  24.1          pyhd8ed1ab_0                       conda-forge
    pandas                     2.2.3         py310ha53a654_1                    conda-forge
    parmed                     4.2.2         py310had63691_1                    conda-forge
    partd                      1.4.2         pyhd8ed1ab_0                       conda-forge
    pcre2                      10.44         h7634a1b_2                         conda-forge
    perl                       5.32.1        7_h10d778d_perl5                   conda-forge
    pillow                     11.0.0        py310h32d1d24_0                    conda-forge
    pint                       0.23          pyhd8ed1ab_1                       conda-forge
    pip                        24.2          pyh8b19718_1                       conda-forge
    pixman                     0.43.4        h73e2aa4_0                         conda-forge
    pluggy                     1.5.0         pyhd8ed1ab_0                       conda-forge
    psutil                     6.0.0         py310hb9d19b6_2                    conda-forge
    pthread-stubs              0.4           h00291cd_1002                      conda-forge
    pycairo                    1.27.0        py310h4d6710c_0                    conda-forge
    pycparser                  2.22          pyhd8ed1ab_0                       conda-forge
    pydantic                   1.10.17       py310h936d840_0                    conda-forge
    pyparsing                  3.2.0         pyhd8ed1ab_1                       conda-forge
    pysocks                    1.7.1         pyha2e5f31_6                       conda-forge
    pytest                     8.3.3         pyhd8ed1ab_0                       conda-forge
    pytest-cov                 5.0.0         pyhd8ed1ab_0                       conda-forge
    pytest-xdist               3.6.1         pyhd8ed1ab_0                       conda-forge
    python                     3.10.15       hd8744da_2_cpython                 conda-forge
    python-constraint          1.4.0         py_0                               conda-forge
    python-dateutil            2.9.0         pyhd8ed1ab_0                       conda-forge
    python-tzdata              2024.2        pyhd8ed1ab_0                       conda-forge
    python_abi                 3.10          5_cp310                            conda-forge
    pytorch                    2.4.1         cpu_mkl_py310h9941b98_102          conda-forge
    pytorch-lightning          2.4.0         pyhd8ed1ab_0                       conda-forge
    pytz                       2024.1        pyhd8ed1ab_0                       conda-forge
    pyyaml                     6.0.2         py310h837254d_1                    conda-forge
    qhull                      2020.2        h3c5361c_5                         conda-forge
    rdkit                      2024.03.5     py310h926f623_3                    conda-forge
    readline                   8.2           h9e318b2_1                         conda-forge
    reportlab                  4.2.5         py310h837254d_0                    conda-forge
    requests                   2.32.3        pyhd8ed1ab_0                       conda-forge
    rlpycairo                  0.2.0         pyhd8ed1ab_0                       conda-forge
    scipy                      1.14.1        py310h9ad1863_1                    conda-forge
    setuptools                 75.1.0        pyhd8ed1ab_0                       conda-forge
    six                        1.16.0        pyh6c4a22f_0                       conda-forge
    sleef                      3.7           h01aa1be_0                         conda-forge
    smirnoff99frosst           1.1.0         pyh44b312d_0                       conda-forge
    snappy                     1.2.1         he1e6707_0                         conda-forge
    sortedcontainers           2.4.0         pyhd8ed1ab_0                       conda-forge
    sqlalchemy                 2.0.36        py310hb9d19b6_0                    conda-forge
    sqlite                     3.46.1        he26b093_0                         conda-forge
    sympy                      1.13.3        pyh2585a3b_104                     conda-forge
    tbb                        2021.13.0     h37c8870_0                         conda-forge
    tblib                      3.0.0         pyhd8ed1ab_0                       conda-forge
    tk                         8.6.13        h1abcd95_1                         conda-forge
    toml                       0.10.2        pyhd8ed1ab_0                       conda-forge
    tomli                      2.0.2         pyhd8ed1ab_0                       conda-forge
    toolz                      1.0.0         pyhd8ed1ab_0                       conda-forge
    torchmetrics               1.4.2         pyhd8ed1ab_0                       conda-forge
    tornado                    6.4.1         py310h837254d_1                    conda-forge
    tqdm                       4.66.5        pyhd8ed1ab_0                       conda-forge
    typing-extensions          4.12.2        hd8ed1ab_0                         conda-forge
    typing_extensions          4.12.2        pyha770c72_0                       conda-forge
    tzdata                     2024b         hc8b5060_0                         conda-forge
    unicodedata2               15.1.0        py310h6729b98_0                    conda-forge
    urllib3                    2.2.3         pyhd8ed1ab_0                       conda-forge
    wheel                      0.44.0        pyhd8ed1ab_0                       conda-forge
    xmltodict                  0.14.2        pyhd8ed1ab_0                       conda-forge
    xorg-libice                1.1.1         h00291cd_1                         conda-forge
    xorg-libsm                 1.2.4         h00291cd_1                         conda-forge
    xorg-libx11                1.8.10        ha6c16c8_0                         conda-forge
    xorg-libxau                1.0.11        h00291cd_1                         conda-forge
    xorg-libxdmcp              1.1.5         h00291cd_0                         conda-forge
    xorg-libxext               1.3.6         h00291cd_0                         conda-forge
    xorg-libxt                 1.3.0         h00291cd_2                         conda-forge
    xorg-xorgproto             2024.1        h00291cd_1                         conda-forge
    xz                         5.2.6         h775f41a_0                         conda-forge
    yaml                       0.2.5         h0d85af4_2                         conda-forge
    zict                       3.0.0         pyhd8ed1ab_0                       conda-forge
    zipp                       3.20.2        pyhd8ed1ab_0                       conda-forge
    zlib                       1.3.1         hd23fc13_2                         conda-forge
    zstandard                  0.23.0        py310h41d873f_1                    conda-forge

Additional context
@lilyminium lilyminium changed the title Failing to assign charges with ambertools on macOS-13 Failing to assign AM1 charges with ambertools on macOS-13 Oct 21, 2024
@lilyminium lilyminium mentioned this issue Oct 22, 2024
Open
This was referenced Oct 24, 2024
Draft
Draft
Draft
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@lilyminium