Description
Hello OpenFE team, recently I have been trying to run absolute hydration free energy simulations for a dataset of molecules, and have managed to do so for different force fields (GAFF, openff) and partial charge methods (am1bcc, NAGL). I wanted to perform calculations with espaloma (both force field and partial charge method) as well, however when I tried to install espaloma_charge as requested on my 1.10.0 openfe env, the Python versioning could not resolve stating that espaloma_charge may only run on 3.12, whereas the default 1.10.0 openfe install is on 3.13.
I then created a new environment where I simultaneously installed openfe and espaloma_charge (I let mamba handle the versioning) and now when I try to run simulations for molecules on the espaloma force field and partial charge method, openfe quickrun errors out due to a JSON encoding error as shown below.
To Reproduce
I create an environment with both openfe and espaloma_charge, then build all transformation JSONs starting from an SDF library. I'll leave an example molecule below that I have been testing on:
mobley_9979854
-OEChem-01201715273D
12 11 0 1 0 0 0 0 0999 V2000
0.3310 1.3650 -0.0660 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0250 -0.0560 -0.4690 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.7470 -0.0300 -1.2930 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5920 -0.8500 0.6890 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7160 -0.2690 1.1640 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.9020 -2.1120 0.3240 F 0 0 0 0 0 0 0 0 0 0 0 0
0.2910 -0.9180 1.7090 F 0 0 0 0 0 0 0 0 0 0 0 0
1.1560 -0.6950 -0.9410 O 0 0 0 0 0 0 0 0 0 0 0 0
1.0530 1.3720 0.7590 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5570 1.9280 0.2400 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8050 1.8910 -0.9010 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9030 -1.5970 -1.1920 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
4 5 1 0 0 0 0
4 6 1 0 0 0 0
4 7 1 0 0 0 0
2 8 1 0 0 0 0
1 9 1 0 0 0 0
1 10 1 0 0 0 0
1 11 1 0 0 0 0
8 12 1 0 0 0 0
M END
> <partial_charges>
-0.100500002503
0.124099999666
0.0688999965787
0.582400023937
-0.23749999702
-0.23749999702
-0.23749999702
-0.574100017548
0.0649000033736
0.0649000033736
0.0649000033736
0.416999995708
> <partial_bond_orders>
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
1.0
> <atom_types>
c3
c3
h1
c3
f
f
f
oh
hc
hc
hc
ho
$$$$
This is the script I run to generate the transformation JSON:
import pathlib
from rdkit import Chem
from openfe import (
SmallMoleculeComponent,
SolventComponent,
ChemicalSystem,
Transformation,
)
from openfe.protocols.openmm_afe import AbsoluteSolvationProtocol
from openff.units import unit
# read sdf files in for ligands
ligands_sdf = Chem.SDMolSupplier("freesolv.sdf", removeHs=False)
ligand_mols = [SmallMoleculeComponent(sdf) for sdf in ligands_sdf]
# solvation
solvent = SolventComponent(positive_ion="K", negative_ion="Cl", neutralize=True)
# protocol - set partial charge model and small molecule forcefield
ahfe_settings = AbsoluteSolvationProtocol.default_settings()
ahfe_settings.partial_charge_settings.partial_charge_method = "espaloma"
ahfe_settings.vacuum_forcefield_settings.small_molecule_forcefield = "espaloma-0.4.0"
ahfe_settings.solvent_forcefield_settings.small_molecule_forcefield = "espaloma-0.4.0"
# gpu device index for parallel computing
ahfe_settings.solvent_engine_settings.gpu_device_index = [0]
ahfe_settings.vacuum_engine_settings.gpu_device_index = [0]
ahfe_protocol = AbsoluteSolvationProtocol(settings=ahfe_settings)
transformation_dir = pathlib.Path("transformations")
transformation_dir.mkdir(exist_ok=True)
for ligand in ligand_mols:
# chemical systems
system_a = ChemicalSystem(
{"ligand": ligand, "solvent": solvent}, name=ligand.name
)
system_b = ChemicalSystem({"solvent": solvent})
transformation = Transformation(
stateA=system_a,
stateB=system_b,
mapping=None,
protocol=ahfe_protocol,
name=f"{system_a.name}",
)
# use openfe CLI to run simulations and gather results
transformation.dump(transformation_dir / f"{transformation.name}.json")When trying to run the simulation, it crashes.
Software versions
- Which operating system and version did you use? The HPC node I'm trying to run the calculations on is on Rocky Linux 9
- Which method did you use to install this package? Env created with mamba
- Copy/paste the output of
conda list (or the equivalent for your package manager):
mamba list output
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────────────────────
_openmp_mutex 4.5 7_kmp_llvm conda-forge
_python_abi3_support 1.0 hd8ed1ab_2 conda-forge
absl-py 2.4.0 pyhd8ed1ab_0 conda-forge
adjusttext 1.3.0 pyhd8ed1ab_0 conda-forge
adwaita-icon-theme 49.0 unix_0 conda-forge
ambertools 24.8 cuda_None_nompi_py312hbe1986e_101 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
anyio 4.13.0 pyhcf101f3_0 conda-forge
argon2-cffi 25.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 25.1.0 py312h4c3975b_2 conda-forge
arpack 3.9.1 nompi_hf03ea27_102 conda-forge
arrow 1.4.0 pyhcf101f3_0 conda-forge
asttokens 3.0.1 pyhd8ed1ab_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_3 conda-forge
async-lru 2.3.0 pyhcf101f3_0 conda-forge
at-spi2-atk 2.38.0 h0630a04_3 conda-forge
at-spi2-core 2.40.3 h0630a04_0 conda-forge
atk-1.0 2.38.0 h04ea711_2 conda-forge
attrs 26.1.0 pyhcf101f3_0 conda-forge
aws-c-auth 0.7.31 h57bd9a3_0 conda-forge
aws-c-cal 0.7.4 hfd43aa1_1 conda-forge
aws-c-common 0.9.28 hb9d3cd8_0 conda-forge
aws-c-compression 0.2.19 h756ea98_1 conda-forge
aws-c-event-stream 0.4.3 h29ce20c_2 conda-forge
aws-c-http 0.8.10 h5e77a74_0 conda-forge
aws-c-io 0.14.18 h2af50b2_12 conda-forge
aws-c-mqtt 0.10.7 h02abb05_0 conda-forge
aws-c-s3 0.6.6 h834ce55_0 conda-forge
aws-c-sdkutils 0.1.19 h756ea98_3 conda-forge
aws-checksums 0.1.20 h756ea98_0 conda-forge
aws-crt-cpp 0.28.3 h3e6eb3e_6 conda-forge
aws-sdk-cpp 1.11.379 h9f1560d_11 conda-forge
babel 2.18.0 pyhcf101f3_1 conda-forge
backports.zstd 1.3.0 py312h90b7ffd_0 conda-forge
beautifulsoup4 4.14.3 pyha770c72_0 conda-forge
biopython 1.87 py312h4c3975b_0 conda-forge
bleach 6.3.0 pyhcf101f3_1 conda-forge
bleach-with-css 6.3.0 hbca2aae_1 conda-forge
blosc 1.21.6 he440d0b_1 conda-forge
brotli 1.2.0 hed03a55_1 conda-forge
brotli-bin 1.2.0 hb03c661_1 conda-forge
brotli-python 1.2.0 py312hdb49522_1 conda-forge
bson 0.5.10 pyhd8ed1ab_0 conda-forge
bzip2 1.0.8 hda65f42_9 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
c-blosc2 2.23.1 hc31b594_0 conda-forge
ca-certificates 2026.4.22 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 7.0.6 pyhd8ed1ab_0 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
certifi 2026.4.22 pyhd8ed1ab_0 conda-forge
cffi 2.0.0 py312h460c074_1 conda-forge
cftime 1.6.5 py312h4f23490_1 conda-forge
charset-normalizer 3.4.7 pyhd8ed1ab_0 conda-forge
cinnabar 0.5.0 pyhd8ed1ab_2 conda-forge
click 8.3.2 pyhc90fa1f_0 conda-forge
click-option-group 0.5.6 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_1 conda-forge
comm 0.2.3 pyhe01879c_0 conda-forge
contourpy 1.3.3 py312h0a2e395_4 conda-forge
cpython 3.12.13 py312hd8ed1ab_0 conda-forge
cuda-nvrtc 13.2.78 hecca717_0 conda-forge
cuda-version 13.2 he2cc418_3 conda-forge
cycler 0.12.1 pyhcf101f3_2 conda-forge
cyrus-sasl 2.1.28 hd9c7081_0 conda-forge
dbus 1.16.2 h24cb091_1 conda-forge
debugpy 1.8.20 py312h8285ef7_0 conda-forge
decorator 5.2.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dgl 2.3.0 py312h0c974e3_0 conda-forge
dill 0.4.1 pyhcf101f3_0 conda-forge
epoxy 1.5.10 hb03c661_2 conda-forge
espaloma_charge 0.0.8 pyhd8ed1ab_3 conda-forge
exceptiongroup 1.3.1 pyhd8ed1ab_0 conda-forge
executing 2.2.1 pyhd8ed1ab_0 conda-forge
fftw 3.3.11 nompi_h3b011a4_100 conda-forge
filelock 3.29.0 pyhd8ed1ab_0 conda-forge
flatbuffers 24.3.25 h59595ed_0 conda-forge
flexcache 0.3 pyhd8ed1ab_1 conda-forge
flexparser 0.4 pyhd8ed1ab_1 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 2.17.1 h27c8c51_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 hc364b38_1 conda-forge
fonttools 4.62.1 py312h8a5da7c_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_1 conda-forge
freetype 2.14.3 ha770c72_0 conda-forge
freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge
fribidi 1.0.16 hb03c661_0 conda-forge
fsspec 2026.3.0 pyhd8ed1ab_0 conda-forge
gast 0.7.0 pyhd8ed1ab_0 conda-forge
gdk-pixbuf 2.44.6 h2b0a6b4_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glib-tools 2.86.4 hf516916_1 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gmpy2 2.3.0 py312hcaba1f9_1 conda-forge
google-pasta 0.2.0 pyhd8ed1ab_2 conda-forge
graphite2 1.3.14 hecca717_2 conda-forge
graphviz 13.1.2 h87b6fe6_0 conda-forge
greenlet 3.4.0 py312h8285ef7_0 conda-forge
griddataformats 1.1.0 pyhd8ed1ab_1 conda-forge
grpcio 1.62.2 py312hb06c811_0 conda-forge
gsd 5.0.1 h7c397b8_0 conda-forge
gtk3 3.24.43 h021d004_4 conda-forge
gts 0.7.6 h977cf35_4 conda-forge
gufe 1.9.0 pyhc364b38_0 conda-forge
h11 0.16.0 pyhcf101f3_1 conda-forge
h2 4.3.0 pyhcf101f3_0 conda-forge
h5py 3.16.0 nompi_py312ha4f8f14_102 conda-forge
harfbuzz 12.2.0 h15599e2_0 conda-forge
hdf4 4.2.15 h2a13503_7 conda-forge
hdf5 1.14.6 nompi_h19486de_106 conda-forge
hicolor-icon-theme 0.17 ha770c72_3 conda-forge
hpack 4.1.0 pyhd8ed1ab_0 conda-forge
httpcore 1.0.9 pyh29332c3_0 conda-forge
httpx 0.28.1 pyhd8ed1ab_0 conda-forge
hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.13 pyhcf101f3_0 conda-forge
importlib-metadata 8.8.0 pyhcf101f3_0 conda-forge
importlib_resources 7.1.0 pyhd8ed1ab_0 conda-forge
iniconfig 2.3.0 pyhd8ed1ab_0 conda-forge
ipycytoscape 1.3.3 pyhd8ed1ab_1 conda-forge
ipykernel 7.2.0 pyha191276_1 conda-forge
ipython 9.12.0 pyhecfbec7_0 conda-forge
ipython_pygments_lexers 1.1.1 pyhd8ed1ab_0 conda-forge
ipywidgets 8.1.8 pyhd8ed1ab_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_1 conda-forge
jax 0.4.31 pyhd8ed1ab_2 conda-forge
jaxlib 0.4.31 cpu_py312h6b2a80f_1 conda-forge
jedi 0.19.2 pyhd8ed1ab_1 conda-forge
jinja2 3.1.6 pyhcf101f3_1 conda-forge
joblib 1.5.3 pyhd8ed1ab_0 conda-forge
jq 1.8.1 h73b1eb8_0 conda-forge
json5 0.14.0 pyhd8ed1ab_0 conda-forge
jsonpointer 3.1.1 pyhcf101f3_0 conda-forge
jsonschema 4.26.0 pyhcf101f3_0 conda-forge
jsonschema-specifications 2025.9.1 pyhcf101f3_0 conda-forge
jsonschema-with-format-nongpl 4.26.0 hcf101f3_0 conda-forge
jupyter-lsp 2.3.1 pyhcf101f3_0 conda-forge
jupyter_client 8.8.0 pyhcf101f3_0 conda-forge
jupyter_core 5.9.1 pyhc90fa1f_0 conda-forge
jupyter_events 0.12.1 pyhcf101f3_0 conda-forge
jupyter_server 2.17.0 pyhcf101f3_0 conda-forge
jupyter_server_terminals 0.5.4 pyhcf101f3_0 conda-forge
jupyterlab 4.5.6 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge
jupyterlab_server 2.28.0 pyhcf101f3_0 conda-forge
jupyterlab_widgets 3.0.16 pyhcf101f3_1 conda-forge
kartograf 1.2.0 pyhd8ed1ab_0 conda-forge
keras 3.11.2 pyh753f3f9_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.5.0 py312h0a2e395_0 conda-forge
konnektor 0.3.0 pyhc364b38_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lark 1.3.1 pyhd8ed1ab_0 conda-forge
lcms2 2.18 h0c24ade_0 conda-forge
ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge
legacy-cgi 2.6.4 pyhcf101f3_0 conda-forge
lerc 4.1.0 hdb68285_0 conda-forge
libabseil 20240116.2 cxx17_he02047a_1 conda-forge
libaec 1.1.5 h088129d_0 conda-forge
libblas 3.9.0 20_linux64_mkl conda-forge
libboost 1.86.0 hed09d94_4 conda-forge
libboost-python 1.86.0 py312hf890105_5 conda-forge
libbrotlicommon 1.2.0 hb03c661_1 conda-forge
libbrotlidec 1.2.0 hb03c661_1 conda-forge
libbrotlienc 1.2.0 hb03c661_1 conda-forge
libcblas 3.9.0 20_linux64_mkl conda-forge
libcufft 12.2.0.46 hecca717_0 conda-forge
libcups 2.3.3 hb8b1518_5 conda-forge
libcurl 8.18.0 h4e3cde8_0 conda-forge
libdeflate 1.25 h17f619e_0 conda-forge
libdrm 2.4.125 hb03c661_1 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
libegl-devel 1.7.0 ha4b6fd6_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.5 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libfreetype 2.14.3 ha770c72_0 conda-forge
libfreetype6 2.14.3 h73754d4_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgd 2.3.3 h6f5c62b_11 conda-forge
libgfortran 15.2.0 h69a702a_18 conda-forge
libgfortran5 15.2.0 h68bc16d_18 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
libgl-devel 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.86.4 h6548e54_1 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libglx-devel 1.7.0 ha4b6fd6_2 conda-forge
libgomp 15.2.0 he0feb66_18 conda-forge
libgrpc 1.62.2 h15f2491_0 conda-forge
libhwloc 2.12.1 default_h3d81e11_1000 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libjpeg-turbo 3.1.4.1 hb03c661_0 conda-forge
liblapack 3.9.0 20_linux64_mkl conda-forge
liblapacke 3.9.0 20_linux64_mkl conda-forge
liblzma 5.8.3 hb03c661_0 conda-forge
libnetcdf 4.9.2 nompi_h21f7587_118 conda-forge
libnghttp2 1.68.1 h877daf1_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libntlm 1.8 hb9d3cd8_0 conda-forge
libpciaccess 0.18 hb9d3cd8_0 conda-forge
libpng 1.6.58 h421ea60_0 conda-forge
libpq 18.1 h5c52fec_2 conda-forge
libprotobuf 4.25.3 hd5b35b9_1 conda-forge
librdkit 2025.09.5 h3c5c181_0 conda-forge
libre2-11 2023.09.01 h5a48ba9_2 conda-forge
librsvg 2.58.4 h49af25d_2 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.53.0 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libtorch 2.3.1 cpu_mkl_h0bb0d08_100 conda-forge
liburing 2.7 h434a139_0 conda-forge
libuuid 2.42 h5347b49_0 conda-forge
libuv 1.51.0 hb03c661_1 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.11.0 he8b52b9_0 conda-forge
libxml2 2.13.9 h04c0eec_0 conda-forge
libxslt 1.1.43 h7a3aeb2_0 conda-forge
libzip 1.11.2 h6991a6a_0 conda-forge
libzlib 1.3.2 h25fd6f3_2 conda-forge
lightning-utilities 0.15.3 pyhd8ed1ab_0 conda-forge
llvm-openmp 22.1.4 h4922eb0_0 conda-forge
llvmlite 0.47.0 py312h7424e68_1 conda-forge
lomap2 3.2.1 pyhd8ed1ab_3 conda-forge
lxml 6.0.2 py312h70dad80_0 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
markdown 3.10.2 pyhcf101f3_0 conda-forge
markdown-it-py 4.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.3 py312h8a5da7c_1 conda-forge
matplotlib-base 3.10.9 py312he3d6523_0 conda-forge
matplotlib-inline 0.2.1 pyhd8ed1ab_0 conda-forge
mda-xdrlib 0.2.0 pyhd8ed1ab_1 conda-forge
mdanalysis 2.10.0 py312hf79963d_1 conda-forge
mdtraj 1.11.1 np2py312h8baca0b_1 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
metis 5.1.1 h59595ed_2 conda-forge
mistune 3.2.0 pyhcf101f3_0 conda-forge
mkl 2023.2.0 ha770c72_50498 conda-forge
ml_dtypes 0.4.0 py312hf9745cd_2 conda-forge
mmtf-python 1.1.3 pyhd8ed1ab_0 conda-forge
mpc 1.4.0 he0a73b1_0 conda-forge
mpfr 4.2.2 he0a73b1_0 conda-forge
mpiplus v0.0.2 pyhd8ed1ab_0 conda-forge
mpmath 1.4.1 pyhd8ed1ab_0 conda-forge
mrcfile 1.5.4 pyhd8ed1ab_0 conda-forge
msgpack-python 1.1.2 py312hd9148b4_1 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
namex 0.1.0 pyhd8ed1ab_0 conda-forge
narwhals 2.20.0 pyhcf101f3_0 conda-forge
nbclient 0.10.4 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.17.1 pyhcf101f3_0 conda-forge
nbformat 5.10.4 pyhd8ed1ab_1 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_1 conda-forge
netcdf-fortran 4.6.2 nompi_h5aa5643_101 conda-forge
netcdf4 1.7.2 nompi_py312hdd76c12_103 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
notebook 7.5.5 pyhcf101f3_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_1 conda-forge
numba 0.65.1 py312hd1dde6f_0 conda-forge
numexpr 2.10.1 mkl_py312h791fadb_2 conda-forge
numpy 1.26.4 py312heda63a1_0 conda-forge
ocl-icd 2.3.3 hb9d3cd8_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
oniguruma 6.9.10 hb9d3cd8_0 conda-forge
opencl-headers 2025.06.13 hecca717_0 conda-forge
openfe 1.10.0 pyhe1070e7_1 conda-forge
openfe-analysis 0.4.0 pyhd8ed1ab_0 conda-forge
openfe-base 1.10.0 pyhc364b38_1 conda-forge
openff-amber-ff-ports 2025.09.0 pyhd8ed1ab_0 conda-forge
openff-forcefields 2026.01.0 pyhd8ed1ab_0 conda-forge
openff-interchange 0.5.2 pyhd8ed1ab_1 conda-forge
openff-interchange-base 0.5.2 pyhd8ed1ab_1 conda-forge
openff-nagl 0.5.5 pyhd8ed1ab_0 conda-forge
openff-nagl-base 0.5.5 pyhd8ed1ab_0 conda-forge
openff-nagl-models 2025.9.0 pyhd8ed1ab_0 conda-forge
openff-toolkit 0.18.0 pyhd8ed1ab_3 conda-forge
openff-toolkit-base 0.18.0 pyhd8ed1ab_3 conda-forge
openff-units 0.3.1 pyhd8ed1ab_2 conda-forge
openff-utilities 0.1.16 pyhd8ed1ab_1 conda-forge
openjpeg 2.5.4 h55fea9a_0 conda-forge
openldap 2.6.10 he970967_0 conda-forge
openmm 8.4.0 py312ha28768a_2 conda-forge
openmmforcefields 0.15.1 pyhcf101f3_1 conda-forge
openmmtools 0.25.3 pyhd8ed1ab_0 conda-forge
openssl 3.6.2 h35e630c_0 conda-forge
opt-einsum 3.4.0 hd8ed1ab_1 conda-forge
opt_einsum 3.4.0 pyhd8ed1ab_1 conda-forge
optree 0.19.0 py312hd9148b4_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_1 conda-forge
packaging 26.1 pyhc364b38_0 conda-forge
pandas 2.3.3 py312hf79963d_1 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.56.4 hadf4263_0 conda-forge
parmed 4.3.1 py312h7ab193c_0 conda-forge
parso 0.8.6 pyhcf101f3_0 conda-forge
patsy 1.0.2 pyhcf101f3_0 conda-forge
pcre2 10.47 haa7fec5_0 conda-forge
pdbfixer 1.12 pyhd8ed1ab_1 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.9.0 pyhd8ed1ab_1 conda-forge
pillow 12.2.0 py312h50c33e8_0 conda-forge
pint 0.24.4 pyhe01879c_2 conda-forge
pip 26.0.1 pyh8b19718_0 conda-forge
pixman 0.46.4 h54a6638_1 conda-forge
platformdirs 4.9.6 pyhcf101f3_0 conda-forge
plotly 6.6.0 pyhd8ed1ab_0 conda-forge
plugcli 0.2.1 pyhd8ed1ab_0 conda-forge
pluggy 1.6.0 pyhf9edf01_1 conda-forge
pooch 1.9.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.25.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.52 pyha770c72_0 conda-forge
protobuf 4.25.3 py312h83439f5_1 conda-forge
psutil 7.1.3 py312h5253ce2_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pyhd8ed1ab_1 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_1 conda-forge
py-cpuinfo 9.0.0 pyhd8ed1ab_1 conda-forge
py3dmol 2.5.4 pyhd8ed1ab_0 conda-forge
pycairo 1.29.0 py312h2596900_1 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pydantic 2.11.10 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.2 py312h680f630_0 conda-forge
pyedr 0.8.0 pyhd8ed1ab_1 conda-forge
pygments 2.20.0 pyhd8ed1ab_0 conda-forge
pygraphviz 1.14 py312hdfa1987_2 conda-forge
pymbar 4.2.0 pyha770c72_2 conda-forge
pymbar-core 4.2.0 pyhd8ed1ab_2 conda-forge
pyparsing 3.3.2 pyhcf101f3_0 conda-forge
pysocks 1.7.1 pyha55dd90_7 conda-forge
pytables 3.11.1 py312hefc0c3f_1 conda-forge
pytest 9.0.3 pyhc364b38_1 conda-forge
pytest-datadir 1.8.0 pyhd8ed1ab_0 conda-forge
pytest-regressions 2.10.0 pyhc455866_0 conda-forge
pytest-rerunfailures 16.1 pyhd8ed1ab_0 conda-forge
python 3.12.13 hd63d673_0_cpython conda-forge
python-constraint 1.4.0 pyhff2d567_1 conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python-fastjsonschema 2.21.2 pyhe01879c_0 conda-forge
python-flatbuffers 25.9.23 pyh1e1bc0e_0 conda-forge
python-gil 3.12.13 hd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python-tzdata 2026.1 pyhd8ed1ab_0 conda-forge
python_abi 3.12 8_cp312 conda-forge
pytng 0.3.4 py312heed6b8f_0 conda-forge
pytorch 2.3.1 cpu_mkl_py312h3b258cc_100 conda-forge
pytorch-lightning 2.6.1 pyhcf101f3_0 conda-forge
pytz 2026.1.post1 pyhcf101f3_0 conda-forge
pyyaml 6.0.3 py312h8a5da7c_1 conda-forge
pyzmq 27.1.0 py312hda471dd_2 conda-forge
qhull 2020.2 h434a139_5 conda-forge
rdkit 2025.09.5 py312h3ecb6ed_0 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.3 h853b02a_0 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
reportlab 4.4.10 pyhcf101f3_1 conda-forge
requests 2.33.1 pyhcf101f3_1 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_1 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rfc3987-syntax 1.1.0 pyhe01879c_1 conda-forge
rich 15.0.0 pyhcf101f3_0 conda-forge
rlpycairo 0.4.0 pyh6c17108_0 conda-forge
rocm-core 7.0.2 h54a6638_0 conda-forge
rpds-py 0.30.0 py312h868fb18_0 conda-forge
s2n 1.5.5 h3931f03_0 conda-forge
scikit-learn 1.8.0 np2py312h3226591_1 conda-forge
scikit-mol 0.6.1 pyhd8ed1ab_0 conda-forge
scipy 1.17.1 py312h54fa4ab_0 conda-forge
seaborn 0.13.2 hd8ed1ab_3 conda-forge
seaborn-base 0.13.2 pyhd8ed1ab_3 conda-forge
send2trash 2.1.0 pyha191276_1 conda-forge
setuptools 82.0.1 pyh332efcf_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
sleef 3.9.0 ha0421bc_0 conda-forge
snappy 1.2.2 h03e3b7b_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_2 conda-forge
soupsieve 2.8.3 pyhd8ed1ab_0 conda-forge
spectate 1.0.1 pyhd8ed1ab_0 conda-forge
sqlalchemy 2.0.49 py312h5253ce2_0 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.6 py312h4f23490_0 conda-forge
sympy 1.14.0 pyh2585a3b_106 conda-forge
tbb 2021.13.0 h8d10470_4 conda-forge
tensorboard 2.17.1 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py312h4eba8b5_4 conda-forge
tensorflow 2.17.0 cpu_py312h69ecde4_2 conda-forge
tensorflow-base 2.17.0 cpu_py312h823dedb_2 conda-forge
tensorflow-estimator 2.17.0 cpu_py312h4f468f2_2 conda-forge
termcolor 3.3.0 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyhc90fa1f_1 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
tidynamics 1.1.2 pyhd8ed1ab_0 conda-forge
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tinydb 4.8.2 pyhd8ed1ab_1 conda-forge
tk 8.6.13 noxft_h366c992_103 conda-forge
tomli 2.4.1 pyhcf101f3_0 conda-forge
torchdata 0.7.1 py312he3f8c6c_7 conda-forge
torchmetrics 1.9.0 pyhd8ed1ab_0 conda-forge
tornado 6.5.5 py312h4c3975b_0 conda-forge
tqdm 4.67.3 pyh8f84b5b_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.2 pyhd8ed1ab_1 conda-forge
typing_extensions 4.15.0 pyhcf101f3_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
unicodedata2 17.0.1 py312h4c3975b_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.6.3 pyhd8ed1ab_0 conda-forge
validators 0.35.0 pyhd8ed1ab_0 conda-forge
wayland 1.25.0 hd6090a7_0 conda-forge
wcwidth 0.6.0 pyhd8ed1ab_0 conda-forge
webcolors 25.10.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.9.0 pyhd8ed1ab_0 conda-forge
werkzeug 3.1.8 pyhcf101f3_0 conda-forge
wheel 0.47.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.15 pyhd8ed1ab_0 conda-forge
wrapt 2.1.2 py312h4c3975b_0 conda-forge
xkeyboard-config 2.47 hb03c661_0 conda-forge
xmltodict 1.0.2 pyhcf101f3_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.13 he1eb515_0 conda-forge
xorg-libxau 1.0.12 hb03c661_1 conda-forge
xorg-libxcomposite 0.4.7 hb03c661_0 conda-forge
xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge
xorg-libxext 1.3.7 hb03c661_0 conda-forge
xorg-libxfixes 6.0.2 hb03c661_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxinerama 1.1.6 hecca717_0 conda-forge
xorg-libxrandr 1.5.5 hb03c661_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xorg-libxxf86vm 1.1.7 hb03c661_0 conda-forge
xorg-xorgproto 2025.1 hb03c661_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
zeromq 4.3.5 h387f397_9 conda-forge
zipp 3.23.1 pyhcf101f3_0 conda-forge
zlib 1.3.2 h25fd6f3_2 conda-forge
zlib-ng 2.3.3 hceb46e0_1 conda-forge
zstandard 0.25.0 py312h5253ce2_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
Output
(paths redacted)
Traceback (most recent call last):
File "/p/project1/project_name/user/mamba/envs/openfe_esp/bin/openfe", line 10, in <module>
sys.exit(main())
^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/click/core.py", line 1485, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/click/core.py", line 1406, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/click/core.py", line 1873, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/click/core.py", line 1269, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/click/core.py", line 824, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/openfecli/utils.py", line 116, in wrapper
result = function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/openfecli/commands/quickrun.py", line 188, in quickrun
json.dump(out_dict, outf, cls=JSON_HANDLER.encoder)
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/__init__.py", line 179, in dump
for chunk in iterable:
^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 432, in _iterencode
yield from _iterencode_dict(o, _current_indent_level)
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 406, in _iterencode_dict
yield from chunks
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 406, in _iterencode_dict
yield from chunks
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 406, in _iterencode_dict
yield from chunks
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 326, in _iterencode_list
yield from chunks
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 326, in _iterencode_list
yield from chunks
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 439, in _iterencode
o = _default(o)
^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/site-packages/gufe/serialization/json.py", line 138, in default
return json.JSONEncoder.default(self, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/p/project1/project_name/user/mamba/envs/openfe_esp/lib/python3.12/json/encoder.py", line 180, in default
raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type OSError is not JSON serializable
Expected behavior
Simulation should run and complete successfully.
Additional context
In past versions I had a similar problem when using espaloma where the formatting of db.json (which I see doesn't exist anymore now?) would break and cause a similar error. When I reformatted the file correctly myself, the simulation could then run successfully. I tried modifying the dag json in the quickrun_cache to see if anything would change but did not have much success. I'm not sure if a similar error is happening elsewhere or if it's something else entirely. I'm a bit short on time so I just decided to ask if you have a workaround.
Thank you and hope to hear from you soon.
Description
Hello OpenFE team, recently I have been trying to run absolute hydration free energy simulations for a dataset of molecules, and have managed to do so for different force fields (GAFF, openff) and partial charge methods (am1bcc, NAGL). I wanted to perform calculations with espaloma (both force field and partial charge method) as well, however when I tried to install espaloma_charge as requested on my 1.10.0 openfe env, the Python versioning could not resolve stating that espaloma_charge may only run on 3.12, whereas the default 1.10.0 openfe install is on 3.13.
I then created a new environment where I simultaneously installed openfe and espaloma_charge (I let mamba handle the versioning) and now when I try to run simulations for molecules on the espaloma force field and partial charge method, openfe quickrun errors out due to a JSON encoding error as shown below.
To Reproduce
I create an environment with both openfe and espaloma_charge, then build all transformation JSONs starting from an SDF library. I'll leave an example molecule below that I have been testing on:
This is the script I run to generate the transformation JSON:
When trying to run the simulation, it crashes.
Software versions
conda list(or the equivalent for your package manager):mamba list output
Output
(paths redacted)
Expected behavior
Simulation should run and complete successfully.
Additional context
In past versions I had a similar problem when using espaloma where the formatting of db.json (which I see doesn't exist anymore now?) would break and cause a similar error. When I reformatted the file correctly myself, the simulation could then run successfully. I tried modifying the dag json in the quickrun_cache to see if anything would change but did not have much success. I'm not sure if a similar error is happening elsewhere or if it's something else entirely. I'm a bit short on time so I just decided to ask if you have a workaround.
Thank you and hope to hear from you soon.