Environment issues

[PabloNA97]

Recently I came across two errors related to openfe dependencies. I leave here the errors and what I did to solve them in case someone else finds it useful. Apologies for not providing the environment.yml files to reproduce the errors easily. Also, I can move this user story to Issues if it's more appropiate...

I installed the openfe environment following the instructions from the webpage. I obtained this environment:

first_openfe_env.txt

Then I created ligand networks and tested a single edge for 3 different systems (one of them I had already ran it before). But this time I obtained the following error:

ForceException: Custom forces not supported. Found force of type CMMotionRemover.

Looking at the stdout file I saw this:

Traceback (most recent call last):
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/gufe/protocols/protocolunit.py", line 322, in execute
    outputs = self._execute(context, **inputs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py", line 1197, in _execute
    outputs = self.run(scratch_basepath=ctx.scratch,
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openfe/protocols/openmm_rfe/equil_rfe_methods.py", line 795, in run
    system_generator.create_system(mol.to_topology().to_openmm(),
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openmmforcefields/generators/system_generators.py", line 400, in create_system
    system = self.forcefield.createSystem(topology, **forcefield_kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openmm/app/forcefield.py", line 1251, in createSystem
    templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openmm/app/forcefield.py", line 1456, in _matchAllResiduesToTemplates
    if generator(self, res):
       ^^^^^^^^^^^^^^^^^^^^
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openmmforcefields/generators/template_generators.py", line 341, in generator
    ffxml_contents = self.generate_residue_template(molecule)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openmmforcefields/generators/template_generators.py", line 1595, in generate_residue_template
    ffxml_contents = self.convert_system_to_ffxml(molecule, system)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/shared/work/pnavarro/envs/openfe/lib/python3.12/site-packages/openmmforcefields/generators/template_generators.py", line 1131, in convert_system_to_ffxml
    raise ForceException(f"Custom forces not supported. Found force of type {force_name}.")
openmmforcefields.generators.template_generators.ForceException: Custom forces not supported. Found force of type CMMotionRemover.

['ForceException', ['Custom forces not supported. Found force of type CMMotionRemover.']]

openfe test was showing the same error. I compared my environment with a previous one and I downgraded openfe, gufe, openmmforcefields and ambertools with:

mamba install openfe=1.1.0 gufe=1.0.0 openmmforcefields=0.14.1 ambertools=23.6

This seemed to work and the error went away. However a new one appeared:

ValueError: Could not locate file amber/ff14SB.xml

I checked the environment and I could find the file in ./lib/python3.12/site-packages/openmmforcefields/ffxml/amber/ff14SB.xml inside the environment folder. The openfe test command show some test failing with the same message related to importlib_* packages. Thus I tried to downgrade them as well:

mamba install "importlib-metadata=8.5.0" "importlib_resources=6.4.5"

Now I have a working environment, I was also able to upgrade openfe back to 1.4.0 and works fine. See both environments exported with the '--no-builds' option to hopefully make them cross-platform compatible :)

Environment with openfe 1.1.0

`channels:

• conda-forge
• defaults
  dependencies:
• _openmp_mutex=4.5
• adjusttext=1.3.0
• adwaita-icon-theme=48.0
• ambertools=23.6
• annotated-types=0.7.0
• anyio=4.9.0
• argon2-cffi=23.1.0
• argon2-cffi-bindings=21.2.0
• arpack=3.9.1
• arrow=1.3.0
• asttokens=3.0.0
• async-lru=2.0.5
• at-spi2-atk=2.38.0
• at-spi2-core=2.40.3
• atk-1.0=2.38.0
• attrs=25.3.0
• babel=2.17.0
• beautifulsoup4=4.13.4
• biopython=1.85
• bleach=6.2.0
• bleach-with-css=6.2.0
• blosc=1.21.6
• brotli=1.1.0
• brotli-bin=1.1.0
• brotli-python=1.1.0
• bson=0.5.10
• bzip2=1.0.8
• c-ares=1.34.5
• c-blosc2=2.17.1
• ca-certificates=2025.4.26
• cached-property=1.5.2
• cached_property=1.5.2
• cachetools=5.5.2
• cairo=1.18.4
• certifi=2025.4.26
• cffi=1.17.1
• cftime=1.6.4
• chardet=5.2.0
• charset-normalizer=3.4.2
• cinnabar=0.4.1
• click=8.2.1
• colorama=0.4.6
• comm=0.2.2
• contourpy=1.3.2
• coverage=7.8.1
• cudatoolkit=11.8.0
• cycler=0.12.1
• cyrus-sasl=2.1.27
• dbus=1.16.2
• debugpy=1.8.14
• decorator=5.2.1
• defusedxml=0.7.1
• dill=0.4.0
• epoxy=1.5.10
• exceptiongroup=1.3.0
• executing=2.2.0
• fftw=3.3.10
• filelock=3.18.0
• font-ttf-dejavu-sans-mono=2.37
• font-ttf-inconsolata=3.000
• font-ttf-source-code-pro=2.038
• font-ttf-ubuntu=0.83
• fontconfig=2.15.0
• fonts-conda-ecosystem=1
• fonts-conda-forge=1
• fonttools=4.58.0
• fqdn=1.5.1
• freetype=2.13.3
• freetype-py=2.3.0
• fribidi=1.0.10
• gdk-pixbuf=2.42.12
• glib-tools=2.84.2
• graphite2=1.3.13
• graphviz=12.2.1
• greenlet=3.2.2
• griddataformats=1.0.2
• gsd=3.4.2
• gtk3=3.24.43
• gts=0.7.6
• gufe=1.0.0
• h11=0.16.0
• h2=4.2.0
• h5py=3.13.0
• harfbuzz=11.2.1
• hdf4=4.2.15
• hdf5=1.14.6
• hicolor-icon-theme=0.17
• hpack=4.1.0
• httpcore=1.0.9
• httpx=0.28.1
• hyperframe=6.1.0
• icu=75.1
• idna=3.10
• importlib-metadata=8.5.0
• importlib_resources=6.4.5
• iniconfig=2.0.0
• ipykernel=6.29.5
• ipython=9.2.0
• ipython_pygments_lexers=1.1.1
• ipywidgets=8.1.7
• isoduration=20.11.0
• jedi=0.19.2
• jinja2=3.1.6
• joblib=1.5.0
• json5=0.12.0
• jsonpointer=3.0.0
• jsonschema=4.23.0
• jsonschema-specifications=2025.4.1
• jsonschema-with-format-nongpl=4.23.0
• jupyter-lsp=2.2.5
• jupyter_client=8.6.3
• jupyter_core=5.7.2
• jupyter_events=0.12.0
• jupyter_server=2.16.0
• jupyter_server_terminals=0.5.3
• jupyterlab=4.4.2
• jupyterlab_pygments=0.3.0
• jupyterlab_server=2.27.3
• jupyterlab_widgets=3.0.15
• kartograf=1.2.0
• keyutils=1.6.1
• kiwisolver=1.4.8
• krb5=1.21.3
• lcms2=2.17
• ld_impl_linux-64=2.43
• lerc=4.0.0
• libaec=1.1.3
• libblas=3.9.0
• libboost=1.84.0
• libboost-python=1.84.0
• libbrotlicommon=1.1.0
• libbrotlidec=1.1.0
• libbrotlienc=1.1.0
• libcblas=3.9.0
• libcups=2.3.3
• libcurl=8.13.0
• libdeflate=1.24
• libedit=3.1.20250104
• libev=4.33
• libexpat=2.7.0
• libffi=3.4.6
• libfreetype=2.13.3
• libfreetype6=2.13.3
• libgcc=15.1.0
• libgcc-ng=15.1.0
• libgd=2.3.3
• libgfortran=15.1.0
• libgfortran-ng=15.1.0
• libgfortran5=15.1.0
• libglib=2.84.2
• libgomp=15.1.0
• libhwloc=2.11.2
• libiconv=1.18
• libjpeg-turbo=3.1.0
• liblapack=3.9.0
• liblzma=5.8.1
• libnetcdf=4.9.2
• libnghttp2=1.64.0
• libnsl=2.0.1
• libntlm=1.8
• libpng=1.6.47
• libpq=17.5
• librdkit=2024.03.6
• librsvg=2.58.4
• libsodium=1.0.20
• libsqlite=3.49.2
• libssh2=1.11.1
• libstdcxx=15.1.0
• libstdcxx-ng=15.1.0
• libtiff=4.7.0
• libuuid=2.38.1
• libwebp-base=1.5.0
• libxcb=1.17.0
• libxcrypt=4.4.36
• libxkbcommon=1.10.0
• libxml2=2.13.8
• libxslt=1.1.39
• libzip=1.11.2
• libzlib=1.3.1
• llvm-openmp=20.1.5
• llvmlite=0.44.0
• lomap2=3.2.1
• lxml=5.4.0
• lz4-c=1.10.0
• markupsafe=3.0.2
• matplotlib-base=3.8.4
• matplotlib-inline=0.1.7
• mda-xdrlib=0.2.0
• mdanalysis=2.9.0
• mdtraj=1.10.3
• mistune=3.1.3
• mkl=2024.2.2
• mmtf-python=1.1.3
• mpiplus=v0.0.2
• mrcfile=1.5.4
• msgpack-python=1.1.0
• munkres=1.1.4
• narwhals=1.40.0
• nbclient=0.10.2
• nbconvert-core=7.16.6
• nbformat=5.10.4
• ncurses=6.5
• nest-asyncio=1.6.0
• netcdf-fortran=4.6.1
• netcdf4=1.7.2
• networkx=3.4.2
• nose=1.3.7
• notebook=7.4.2
• notebook-shim=0.2.4
• numba=0.61.2
• numexpr=2.10.2
• numpy=1.26.4
• ocl-icd=2.3.3
• ocl-icd-system=1.0.0
• opencl-headers=2024.10.24
• openfe=1.1.0
• openfe-analysis=0.2.0
• openff-amber-ff-ports=0.0.4
• openff-forcefields=2024.09.0
• openff-interchange=0.4.1
• openff-interchange-base=0.4.1
• openff-models=0.1.2
• openff-toolkit=0.16.9
• openff-toolkit-base=0.16.9
• openff-units=0.2.2
• openff-utilities=0.1.15
• openjpeg=2.5.3
• openldap=2.6.9
• openmm=8.1.2
• openmmforcefields=0.14.1
• openmmtools=0.23.1
• openssl=3.5.0
• overrides=7.7.0
• packaging=25.0
• pandas=2.2.3
• pandocfilters=1.5.0
• panedr=0.8.0
• pango=1.56.3
• parmed=4.3.0
• parso=0.8.4
• patsy=1.0.1
• pcre2=10.45
• pdbfixer=1.9
• perl=5.32.1
• pexpect=4.9.0
• pickleshare=0.7.5
• pillow=11.2.1
• pint=0.23
• pip=25.1.1
• pixman=0.46.0
• pkgutil-resolve-name=1.3.10
• platformdirs=4.3.8
• plotly=6.1.1
• plugcli=0.2.0
• pluggy=1.6.0
• pooch=1.8.2
• prometheus_client=0.22.0
• prompt-toolkit=3.0.51
• psutil=7.0.0
• pthread-stubs=0.4
• ptyprocess=0.7.0
• pure_eval=0.2.3
• py-cpuinfo=9.0.0
• py3dmol=2.4.2
• pycairo=1.28.0
• pycparser=2.22
• pydantic=2.11.4
• pydantic-core=2.33.2
• pyedr=0.8.0
• pygments=2.19.1
• pygraphviz=1.14
• pymbar=3.1.1
• pyparsing=3.2.3
• pysocks=1.7.1
• pytables=3.10.2
• pytest=8.3.5
• python=3.12.10
• python-constraint=1.4.0
• python-dateutil=2.9.0.post0
• python-fastjsonschema=2.21.1
• python-json-logger=2.0.7
• python-tzdata=2025.2
• python_abi=3.12
• pytng=0.3.3
• pytz=2025.2
• pyyaml=6.0.2
• pyzmq=26.4.0
• rdkit=2024.03.5
• readline=8.2
• referencing=0.36.2
• reportlab=4.4.1
• requests=2.32.3
• rfc3339-validator=0.1.4
• rfc3986-validator=0.1.1
• rlpycairo=0.2.0
• rpds-py=0.25.1
• scikit-learn=1.6.1
• scipy=1.15.2
• seaborn=0.13.2
• seaborn-base=0.13.2
• send2trash=1.8.3
• setuptools=80.8.0
• six=1.17.0
• smirnoff99frosst=1.1.0
• snappy=1.2.1
• sniffio=1.3.1
• soupsieve=2.7
• sqlalchemy=2.0.41
• stack_data=0.6.3
• statsmodels=0.14.4
• tbb=2021.13.0
• terminado=0.18.1
• threadpoolctl=3.6.0
• tidynamics=1.1.2
• tinycss2=1.4.0
• tinydb=4.8.2
• tk=8.6.13
• tomli=2.2.1
• tornado=6.5
• tqdm=4.67.1
• traitlets=5.14.3
• types-python-dateutil=2.9.0.20250516
• typing-extensions=4.13.2
• typing-inspection=0.4.1
• typing_extensions=4.13.2
• typing_utils=0.1.0
• tzdata=2025b
• unicodedata2=16.0.0
• uri-template=1.3.0
• urllib3=2.4.0
• validators=0.35.0
• wayland=1.23.1
• wcwidth=0.2.13
• webcolors=24.11.1
• webencodings=0.5.1
• websocket-client=1.8.0
• wheel=0.45.1
• widgetsnbextension=4.0.14
• xkeyboard-config=2.44
• xmltodict=0.14.2
• xorg-libice=1.1.2
• xorg-libsm=1.2.6
• xorg-libx11=1.8.12
• xorg-libxau=1.0.12
• xorg-libxcomposite=0.4.6
• xorg-libxcursor=1.2.3
• xorg-libxdamage=1.1.6
• xorg-libxdmcp=1.1.5
• xorg-libxext=1.3.6
• xorg-libxfixes=6.0.1
• xorg-libxi=1.8.2
• xorg-libxinerama=1.1.5
• xorg-libxrandr=1.5.4
• xorg-libxrender=0.9.12
• xorg-libxt=1.3.1
• xorg-libxtst=1.2.5
• yaml=0.2.5
• zeromq=4.3.5
• zipp=3.21.0
• zlib=1.3.1
• zlib-ng=2.2.4
• zstandard=0.23.0
• zstd=1.5.7
• pip:
  • amberutils==21.0
  • edgembar==0.2
  • mmpbsa-py==16.0
  • packmol-memgen==2024.2.9
  • pdb4amber==22.0
  • pymsmt==22.0
  • pytraj==2.0.6
  • sander==22.0
    `

Environment with openfe 1.4.0

`channels:

• conda-forge
• defaults
  dependencies:
• _openmp_mutex=4.5
• adjusttext=1.3.0
• adwaita-icon-theme=48.0
• ambertools=23.6
• annotated-types=0.7.0
• anyio=4.9.0
• argon2-cffi=23.1.0
• argon2-cffi-bindings=21.2.0
• arpack=3.9.1
• arrow=1.3.0
• asttokens=3.0.0
• async-lru=2.0.5
• at-spi2-atk=2.38.0
• at-spi2-core=2.40.3
• atk-1.0=2.38.0
• attrs=25.3.0
• babel=2.17.0
• beautifulsoup4=4.13.4
• biopython=1.85
• bleach=6.2.0
• bleach-with-css=6.2.0
• blosc=1.21.6
• brotli=1.1.0
• brotli-bin=1.1.0
• brotli-python=1.1.0
• bson=0.5.10
• bzip2=1.0.8
• c-ares=1.34.5
• c-blosc2=2.17.1
• ca-certificates=2025.4.26
• cached-property=1.5.2
• cached_property=1.5.2
• cachetools=5.5.2
• cairo=1.18.4
• certifi=2025.4.26
• cffi=1.17.1
• cftime=1.6.4
• chardet=5.2.0
• charset-normalizer=3.4.2
• cinnabar=0.4.1
• click=8.1.8
• colorama=0.4.6
• comm=0.2.2
• contourpy=1.3.2
• coverage=7.8.1
• cudatoolkit=11.8.0
• cycler=0.12.1
• cyrus-sasl=2.1.27
• dbus=1.16.2
• debugpy=1.8.14
• decorator=5.2.1
• defusedxml=0.7.1
• dill=0.4.0
• epoxy=1.5.10
• exceptiongroup=1.3.0
• executing=2.2.0
• fftw=3.3.10
• filelock=3.18.0
• flexcache=0.3
• flexparser=0.4
• font-ttf-dejavu-sans-mono=2.37
• font-ttf-inconsolata=3.000
• font-ttf-source-code-pro=2.038
• font-ttf-ubuntu=0.83
• fontconfig=2.15.0
• fonts-conda-ecosystem=1
• fonts-conda-forge=1
• fonttools=4.58.0
• fqdn=1.5.1
• freetype=2.13.3
• freetype-py=2.3.0
• fribidi=1.0.10
• gdk-pixbuf=2.42.12
• glib-tools=2.84.2
• graphite2=1.3.13
• graphviz=12.2.1
• greenlet=3.2.2
• griddataformats=1.0.2
• gsd=3.4.2
• gtk3=3.24.43
• gts=0.7.6
• gufe=1.4.1
• h11=0.16.0
• h2=4.2.0
• h5py=3.13.0
• harfbuzz=11.2.1
• hdf4=4.2.15
• hdf5=1.14.6
• hicolor-icon-theme=0.17
• hpack=4.1.0
• httpcore=1.0.9
• httpx=0.28.1
• hyperframe=6.1.0
• icu=75.1
• idna=3.10
• importlib-metadata=8.5.0
• importlib_resources=6.4.5
• iniconfig=2.0.0
• ipykernel=6.29.5
• ipython=9.2.0
• ipython_pygments_lexers=1.1.1
• ipywidgets=8.1.7
• isoduration=20.11.0
• jax=0.5.2
• jaxlib=0.5.2
• jedi=0.19.2
• jinja2=3.1.6
• joblib=1.5.0
• json5=0.12.0
• jsonpointer=3.0.0
• jsonschema=4.23.0
• jsonschema-specifications=2025.4.1
• jsonschema-with-format-nongpl=4.23.0
• jupyter-lsp=2.2.5
• jupyter_client=8.6.3
• jupyter_core=5.7.2
• jupyter_events=0.12.0
• jupyter_server=2.16.0
• jupyter_server_terminals=0.5.3
• jupyterlab=4.4.2
• jupyterlab_pygments=0.3.0
• jupyterlab_server=2.27.3
• jupyterlab_widgets=3.0.15
• kartograf=1.2.0
• keyutils=1.6.1
• kiwisolver=1.4.8
• krb5=1.21.3
• lcms2=2.17
• ld_impl_linux-64=2.43
• lerc=4.0.0
• libabseil=20250127.1
• libaec=1.1.3
• libblas=3.9.0
• libboost=1.84.0
• libboost-python=1.84.0
• libbrotlicommon=1.1.0
• libbrotlidec=1.1.0
• libbrotlienc=1.1.0
• libcblas=3.9.0
• libcups=2.3.3
• libcurl=8.13.0
• libdeflate=1.24
• libedit=3.1.20250104
• libev=4.33
• libexpat=2.7.0
• libffi=3.4.6
• libfreetype=2.13.3
• libfreetype6=2.13.3
• libgcc=15.1.0
• libgcc-ng=15.1.0
• libgd=2.3.3
• libgfortran=15.1.0
• libgfortran-ng=15.1.0
• libgfortran5=15.1.0
• libglib=2.84.2
• libgomp=15.1.0
• libgrpc=1.71.0
• libhwloc=2.11.2
• libiconv=1.18
• libjpeg-turbo=3.1.0
• liblapack=3.9.0
• liblzma=5.8.1
• libnetcdf=4.9.2
• libnghttp2=1.64.0
• libnsl=2.0.1
• libntlm=1.8
• libpng=1.6.47
• libpq=17.5
• libprotobuf=5.29.3
• librdkit=2024.03.6
• libre2-11=2024.07.02
• librsvg=2.58.4
• libsodium=1.0.20
• libsqlite=3.49.2
• libssh2=1.11.1
• libstdcxx=15.1.0
• libstdcxx-ng=15.1.0
• libtiff=4.7.0
• libuuid=2.38.1
• libwebp-base=1.5.0
• libxcb=1.17.0
• libxcrypt=4.4.36
• libxkbcommon=1.10.0
• libxml2=2.13.8
• libxslt=1.1.39
• libzip=1.11.2
• libzlib=1.3.1
• llvm-openmp=20.1.5
• llvmlite=0.44.0
• lomap2=3.2.1
• lxml=5.4.0
• lz4-c=1.10.0
• markdown-it-py=3.0.0
• markupsafe=3.0.2
• matplotlib-base=3.8.4
• matplotlib-inline=0.1.7
• mda-xdrlib=0.2.0
• mdanalysis=2.9.0
• mdtraj=1.10.3
• mdurl=0.1.2
• mistune=3.1.3
• mkl=2024.2.2
• ml_dtypes=0.5.1
• mmtf-python=1.1.3
• mpiplus=v0.0.2
• mrcfile=1.5.4
• msgpack-python=1.1.0
• munkres=1.1.4
• narwhals=1.40.0
• nbclient=0.10.2
• nbconvert-core=7.16.6
• nbformat=5.10.4
• ncurses=6.5
• nest-asyncio=1.6.0
• netcdf-fortran=4.6.1
• netcdf4=1.7.2
• networkx=3.4.2
• nose=1.3.7
• notebook=7.4.2
• notebook-shim=0.2.4
• numba=0.61.2
• numexpr=2.10.2
• numpy=1.26.4
• ocl-icd=2.3.3
• ocl-icd-system=1.0.0
• opencl-headers=2024.10.24
• openfe=1.4.0
• openfe-analysis=0.3.1
• openff-amber-ff-ports=0.0.4
• openff-forcefields=2024.09.0
• openff-interchange=0.4.2
• openff-interchange-base=0.4.2
• openff-models=0.1.2
• openff-toolkit=0.16.9
• openff-toolkit-base=0.16.9
• openff-units=0.3.1
• openff-utilities=0.1.15
• openjpeg=2.5.3
• openldap=2.6.9
• openmm=8.1.2
• openmmforcefields=0.14.2
• openmmtools=0.24.2
• openssl=3.5.0
• opt_einsum=3.4.0
• overrides=7.7.0
• packaging=25.0
• pandas=2.2.3
• pandocfilters=1.5.0
• panedr=0.8.0
• pango=1.56.3
• parmed=4.3.0
• parso=0.8.4
• patsy=1.0.1
• pcre2=10.45
• pdbfixer=1.9
• perl=5.32.1
• pexpect=4.9.0
• pickleshare=0.7.5
• pillow=11.2.1
• pint=0.24.4
• pip=25.1.1
• pixman=0.46.0
• pkgutil-resolve-name=1.3.10
• platformdirs=4.3.8
• plotly=6.1.1
• plugcli=0.2.0
• pluggy=1.6.0
• pooch=1.8.2
• prometheus_client=0.22.0
• prompt-toolkit=3.0.51
• psutil=7.0.0
• pthread-stubs=0.4
• ptyprocess=0.7.0
• pure_eval=0.2.3
• py-cpuinfo=9.0.0
• py3dmol=2.4.2
• pycairo=1.28.0
• pycparser=2.22
• pydantic=2.11.4
• pydantic-core=2.33.2
• pyedr=0.8.0
• pygments=2.19.1
• pygraphviz=1.14
• pymbar=4.0.3
• pymbar-core=4.0.3
• pyparsing=3.2.3
• pysocks=1.7.1
• pytables=3.10.2
• pytest=8.3.5
• pytest-datadir=1.6.1
• pytest-regressions=2.7.0
• python=3.12.10
• python-constraint=1.4.0
• python-dateutil=2.9.0.post0
• python-fastjsonschema=2.21.1
• python-json-logger=2.0.7
• python-tzdata=2025.2
• python_abi=3.12
• pytng=0.3.3
• pytz=2025.2
• pyyaml=6.0.2
• pyzmq=26.4.0
• rdkit=2024.03.5
• re2=2024.07.02
• readline=8.2
• referencing=0.36.2
• reportlab=4.4.1
• requests=2.32.3
• rfc3339-validator=0.1.4
• rfc3986-validator=0.1.1
• rich=14.0.0
• rlpycairo=0.2.0
• rpds-py=0.25.1
• scikit-learn=1.6.1
• scipy=1.15.2
• seaborn=0.13.2
• seaborn-base=0.13.2
• send2trash=1.8.3
• setuptools=80.8.0
• six=1.17.0
• smirnoff99frosst=1.1.0
• snappy=1.2.1
• sniffio=1.3.1
• soupsieve=2.7
• sqlalchemy=2.0.41
• stack_data=0.6.3
• statsmodels=0.14.4
• tbb=2021.13.0
• terminado=0.18.1
• threadpoolctl=3.6.0
• tidynamics=1.1.2
• tinycss2=1.4.0
• tinydb=4.8.2
• tk=8.6.13
• tomli=2.2.1
• tornado=6.5
• tqdm=4.67.1
• traitlets=5.14.3
• types-python-dateutil=2.9.0.20250516
• typing-extensions=4.13.2
• typing-inspection=0.4.1
• typing_extensions=4.13.2
• typing_utils=0.1.0
• tzdata=2025b
• unicodedata2=16.0.0
• uri-template=1.3.0
• urllib3=2.4.0
• validators=0.35.0
• wayland=1.23.1
• wcwidth=0.2.13
• webcolors=24.11.1
• webencodings=0.5.1
• websocket-client=1.8.0
• wheel=0.45.1
• widgetsnbextension=4.0.14
• xkeyboard-config=2.44
• xmltodict=0.14.2
• xorg-libice=1.1.2
• xorg-libsm=1.2.6
• xorg-libx11=1.8.12
• xorg-libxau=1.0.12
• xorg-libxcomposite=0.4.6
• xorg-libxcursor=1.2.3
• xorg-libxdamage=1.1.6
• xorg-libxdmcp=1.1.5
• xorg-libxext=1.3.6
• xorg-libxfixes=6.0.1
• xorg-libxi=1.8.2
• xorg-libxinerama=1.1.5
• xorg-libxrandr=1.5.4
• xorg-libxrender=0.9.12
• xorg-libxt=1.3.1
• xorg-libxtst=1.2.5
• yaml=0.2.5
• zeromq=4.3.5
• zipp=3.21.0
• zlib=1.3.1
• zlib-ng=2.2.4
• zstandard=0.23.0
• zstd=1.5.7
• pip:
  • amberutils==21.0
  • edgembar==0.2
  • mmpbsa-py==16.0
  • packmol-memgen==2024.2.9
  • pdb4amber==22.0
  • pymsmt==22.0
  • pytraj==2.0.6
  • sander==22.0
    `

Hope it's useful to someone!

[IAlibay]

Thanks for reporting this @PabloNA97

Overall, we do not recommend downgrading and re-upgrading. I'm glad to see that it works for you in this instance, but this is far too error prone. Ideally we want to make sure it works when you install things the first time around.

The first issue you mention (re: CMMotionRemover) is something that is fixed in OpenMMForceFields 0.14.2. It's interesting to see that your first environment didn't pick this up. Could I ask how you installed that environment? Was it just "mamba install openfe"?

The second issue you mention seems to maybe be related to a know issue that happened with importllib-metadata yesterday: conda-forge/importlib_metadata-feedstock#148

I'm wondering if retrying a fresh environment today might fix some of these issues.

I'm going to tag @atravitz and @mikemhenry here - it looks like the conda_cron CI jobs passed fine yesterday, but I'm not sure if there's more double checking we should be doing to see if clean installs are working fine.

[PabloNA97]

Hi @IAlibay

Thank you for the feedback, I'll take this into account!

My first attempt involved upgrading an older environment to openfe=1.4.0 and kartograf=1.2.0 with mamba install. Then if I remember correctly I re-installed the whole environment from scratch using:

mamba create -c conda-forge -p /path/to/env/openfe openfe=1.4.0 kartograf=1.2

Both gave me the CMMotionRemover error. This was a clean installation in principle and no base environment was active - not sure what happened. From what you say it doesn't make sense that it went away downgrading openmmforcefields. If you cannot reproduce it it might be a mistake on my end.

Thanks for all the work you do here by the way :)

[IAlibay]

Thanks for the extra info!

We really want to make sure it works first time for you, so we'll triage this and see if there's anything we can do to make things less painful!

As a more immediate fix, we do have a conda-lock file (you can see it in the release assets here: https://github.com/OpenFreeEnergy/openfe/releases/tag/v1.4.0 and instructions here: https://docs.openfree.energy/en/latest/installation.html#reproducible-builds-with-a-conda-lock-file). I would strongly recommend using it, it has made my life a ton easier when getting deployment versions of OpenFE up, so hopefully it might be useful to you too!

[PabloNA97]

Will keep this at hand, thanks a lot @IAlibay !