Hello, I was trying to do an RBFE calculation with a 2 ligands transformation.
RBFE-NETWORK PLANNER
______________________
Parsing in Files:
Got input:
Small Molecules: SmallMoleculeComponent(name=SE1) SmallMoleculeComponent(name=SE2)
Protein: ProteinComponent(name=)
Cofactors: [SmallMoleculeComponent(name=obj01)]
Solvent: SolventComponent(name=O, Na+, Cl-)
Using Options:
Mapper: <KartografAtomMapper-92be13375caab9a5f2ecbf75d925982f>
Mapping Scorer: <function default_lomap_score at 0x7ff605b98220>
Network Generation: <function generate_minimal_spanning_network at 0x7ff604b06e80>
Partial Charge Generation: am1bcc
n_protocol_repeats=1 (1 simulation repeat(s) per transformation)
Planning RBFE-Campaign:
assigning ligand partial charges -- this may be slow
Generating charges: 100%|█████████████████████████| 2/2 [00:19<00:00, 9.66s/it]
assigning cofactor partial charges -- this may be slow
Generating charges: 100%|█████████████████████████| 1/1 [00:13<00:00, 13.59s/it]
Done
Output:
Saving to: /common/workdir/fep/network_setup
- network_setup.json
- ligand_network.graphml
- rbfe_SE1_complex_SE2_complex.json
- rbfe_SE1_solvent_SE2_solvent.json
Duration: 0:00:39.836281
(openfe) [root@pipeline-3905 fep]# openfe quickrun network_setup/transformations/rbfe_SE1_solvent_SE2_solvent.json -o results/rbfe_SE1_solvent_SE2_solvent.json -d results/rbfe_SE1_so
lvent_SE2_solvent
Loading file...
Planning simulations for this edge...
Element change in mapping between atoms Ligand A: 25 (element 16) and Ligand B: 25 (element 8)
No mass scaling is attempted in the hybrid topology, the average mass of the two atoms will be used in the simulation
Starting the simulations for this edge...
An online_analysis_interval that is not a multiple of the checkpoint_interval can lead to redundant information in the real time yaml file after recovering from checkpoints.
Please cite the following:
Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processin
g unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209
Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27
Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413
Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. D
OI: 10.1021/ct900463w
Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. D
OI:10.1063/1.3660669
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 0 attempts of integration with move LangevinDynamicsMove Attempting a restart...
Potential energy is NaN after 1 attempts of integration with move LangevinDynamicsMove Attempting a restart...
(openfe) [root@pipeline-3905 fep]# micromamba list
List of packages in environment: "/opt/py/mamba/PyLib_Common/envs/openfe"
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────────────────────
_openmp_mutex 4.5 7_kmp_llvm conda-forge
_python_abi3_support 1.0 hd8ed1ab_2 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_py313hb0f039c_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 py313h07c4f96_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
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
babel 2.18.0 pyhcf101f3_1 conda-forge
backports.zstd 1.5.0 py313h18e8e13_0 conda-forge
beautifulsoup4 4.14.3 pyha770c72_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 py313hf159716_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 3.0.3 hc31b594_0 conda-forge
ca-certificates 2026.5.20 hbd8a1cb_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 7.1.3 pyhd8ed1ab_0 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
certifi 2026.5.20 pyhd8ed1ab_0 conda-forge
cffi 2.0.0 py313hf46b229_1 conda-forge
cftime 1.6.5 py313h29aa505_1 conda-forge
charset-normalizer 3.4.7 pyhd8ed1ab_0 conda-forge
cinnabar 0.5.0 pyhd8ed1ab_2 conda-forge
click 8.4.0 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 py313hc8edb43_4 conda-forge
cpython 3.13.13 py313hd8ed1ab_100 conda-forge
cuda-version 11.8 h70ddcb2_3 conda-forge
cudatoolkit 11.8.0 h4ba93d1_13 conda-forge
cudnn 9.10.1.4 haad7af6_0 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 py313h5d5ffb9_0 conda-forge
decorator 5.3.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dill 0.4.1 pyhcf101f3_0 conda-forge
epoxy 1.5.10 hb03c661_2 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
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 4.63.0 py313h3dea7bd_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 2026.4.0 pyhd8ed1ab_0 conda-forge
gdk-pixbuf 2.44.6 h2b0a6b4_0 conda-forge
glib-tools 2.88.1 hee1de02_2 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gmpy2 2.3.0 py313h86d8783_1 conda-forge
graphite2 1.3.14 hecca717_2 conda-forge
graphviz 13.1.2 h87b6fe6_0 conda-forge
greenlet 3.5.1 py313h5d5ffb9_0 conda-forge
griddataformats 1.1.0 pyhd8ed1ab_1 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 1.8.0 pyhcf101f3_2 conda-forge
h11 0.16.0 pyhcf101f3_1 conda-forge
h2 4.3.0 pyhcf101f3_0 conda-forge
h5py 3.16.0 nompi_py313h253c126_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 3.15 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
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ipython 9.13.0 pyh53cf698_0 conda-forge
ipython_pygments_lexers 1.1.1 pyhd8ed1ab_0 conda-forge
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jax 0.9.0 pyhd8ed1ab_0 conda-forge
jaxlib 0.9.0 cpu_py313h7c752d1_0 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 2.18.2 pyhcf101f3_0 conda-forge
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jupyterlab 4.5.7 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
kernel-headers_linux-64 4.18.0 he073ed8_9 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.5.0 py313hc8edb43_0 conda-forge
konnektor 0.3.0 pyhc364b38_0 conda-forge
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lcms2 2.19.1 h0c24ade_0 conda-forge
ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge
legacy-cgi 2.6.4 pyh742d864_0 conda-forge
lerc 4.1.0 hdb68285_0 conda-forge
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libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
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libffi 3.5.2 h3435931_0 conda-forge
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libgcc 15.2.0 he0feb66_19 conda-forge
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libgd 2.3.3 h6f5c62b_11 conda-forge
libgfortran 15.2.0 h69a702a_19 conda-forge
libgfortran5 15.2.0 h68bc16d_19 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
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libglib 2.88.1 h0d30a3d_2 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_19 conda-forge
libgrpc 1.73.1 h3288cfb_1 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 3.11.0 6_h5e43f62_mkl conda-forge
liblzma 5.8.3 hb03c661_0 conda-forge
libmagma 2.9.0 h45b15fe_0 conda-forge
libmpdec 4.0.0 hb03c661_1 conda-forge
libnetcdf 4.9.2 nompi_h21f7587_118 conda-forge
libnghttp2 1.68.1 h877daf1_0 conda-forge
libnl 3.11.0 hb9d3cd8_0 conda-forge
libntlm 1.8 hb9d3cd8_0 conda-forge
libpciaccess 0.19 hb03c661_0 conda-forge
libpng 1.6.58 h421ea60_0 conda-forge
libpq 18.1 h5c52fec_2 conda-forge
libprotobuf 6.31.1 h49aed37_4 conda-forge
librdkit 2025.09.5 h3c5c181_0 conda-forge
libre2-11 2025.11.05 h7b12aa8_0 conda-forge
librsvg 2.58.4 h49af25d_2 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.53.1 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_19 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_19 conda-forge
libsystemd0 257.13 hd0affe5_0 conda-forge
libtiff 4.7.1 h9d88235_1 conda-forge
libtorch 2.8.0 cpu_mkl_h09b866c_102 conda-forge
libudev1 257.13 hd0affe5_0 conda-forge
libuuid 2.42.1 h5347b49_0 conda-forge
libuv 1.52.1 h280c20c_0 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 22.1.6 h4922eb0_0 conda-forge
llvmlite 0.47.0 py313hdd307be_1 conda-forge
lomap2 3.2.1 pyhd8ed1ab_3 conda-forge
lxml 6.0.2 py313h6b0e12e_0 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
markdown-it-py 4.2.0 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.3 py313h3dea7bd_1 conda-forge
matplotlib-base 3.10.9 py313h683a580_0 conda-forge
matplotlib-inline 0.2.2 pyhd8ed1ab_0 conda-forge
mda-xdrlib 0.2.0 pyhd8ed1ab_1 conda-forge
mdanalysis 2.10.0 py313h08cd8bf_1 conda-forge
mdtraj 1.11.1 np2py313h48ae260_1 conda-forge
mdurl 0.1.2 pyhd8ed1ab_1 conda-forge
mistune 3.2.1 pyhcf101f3_0 conda-forge
mkl 2025.3.1 h0e700b2_12 conda-forge
ml_dtypes 0.5.4 np2py313h73dcb5b_1 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 py313h7037e92_1 conda-forge
munkres 1.1.4 pyhd8ed1ab_1 conda-forge
narwhals 2.21.2 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
nccl 2.27.3.1 h03a54cd_0 conda-forge
ncurses 6.6 hdb14827_0 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_py313ha67fc0a_103 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
notebook 7.5.6 pyhcf101f3_1 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_1 conda-forge
numba 0.65.1 py313h5dce7c4_1 conda-forge
numexpr 2.14.1 mkl_py313hddce2c6_1 conda-forge
numpy 2.3.5 py313hf6604e3_1 conda-forge
ocl-icd 2.3.3 hb9d3cd8_0 conda-forge
ocl-icd-system 1.0.0 1 conda-forge
onemkl-license 2025.3.1 hf2ce2f3_12 conda-forge
oniguruma 6.9.10 hb9d3cd8_0 conda-forge
opencl-headers 2025.06.13 hecca717_0 conda-forge
openfe 1.9.1 pyh2aa6593_5 conda-forge
openfe-analysis 0.4.0 pyhd8ed1ab_0 conda-forge
openfe-base 1.9.1 pyhc364b38_5 conda-forge
openff-amber-ff-ports 2025.09.0 pyhd8ed1ab_0 conda-forge
openff-forcefields 2026.01.0 pyhd8ed1ab_0 conda-forge
openff-interchange 0.5.3 pyhd8ed1ab_1 conda-forge
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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-packmol 0.1 pyhc364b38_1 conda-forge
openff-toolkit 0.18.0 pyhd8ed1ab_3 conda-forge
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openldap 2.6.10 he970967_0 conda-forge
openmm 8.2.0 py313h489b4b4_3 conda-forge
openmmforcefields 0.15.1 pyhcf101f3_1 conda-forge
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openssl 3.6.2 h35e630c_0 conda-forge
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optree 0.19.1 py313h7037e92_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_1 conda-forge
packaging 26.2 pyhc364b38_0 conda-forge
pandas 2.3.3 py313h08cd8bf_2 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
pango 1.56.4 hadf4263_0 conda-forge
parmed 4.3.1 py313hc4ed87d_1 conda-forge
parso 0.8.7 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 py313h80991f8_0 conda-forge
pint 0.24.4 pyhe01879c_2 conda-forge
pip 26.1.1 pyh145f28c_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
psutil 7.1.3 py313h54dd161_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
pybind11 2.13.6 pyhc790b64_3 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pybind11-global 2.13.6 pyh217bc35_3 conda-forge
pycairo 1.29.0 py313h3f29d12_1 conda-forge
pycparser 3.0 pyhcf101f3_0 conda-forge
pydantic 2.11.10 pyh3cfb1c2_0 conda-forge
pydantic-core 2.33.2 py313h4b2b08d_0 conda-forge
pyedr 0.8.0 pyhd8ed1ab_1 conda-forge
pygments 2.20.0 pyhd8ed1ab_0 conda-forge
pygraphviz 1.14 py313h45fd7b0_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 py313h0546747_2 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 16.2 pyhd8ed1ab_0 conda-forge
python 3.13.13 h6add32d_100_cp313 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-gil 3.13.13 h4df99d1_100 conda-forge
python-json-logger 3.2.1 pyh332efcf_0 conda-forge
python-tzdata 2026.2 pyhd8ed1ab_0 conda-forge
python_abi 3.13 8_cp313 conda-forge
pytng 0.3.4 py313h75f1e36_0 conda-forge
pytorch 2.8.0 cpu_mkl_py313_h19d87ba_102 conda-forge
pytorch-lightning 2.6.1 pyhcf101f3_0 conda-forge
pytz 2026.2 pyhcf101f3_0 conda-forge
pyyaml 6.0.3 py313h3dea7bd_1 conda-forge
pyzmq 27.1.0 py312hda471dd_2 conda-forge
qhull 2020.2 h434a139_5 conda-forge
rdkit 2025.09.5 py313h66a1ddb_0 conda-forge
rdma-core 63.0 h192683f_1 conda-forge
re2 2025.11.05 h5301d42_0 conda-forge
readline 8.3 h853b02a_0 conda-forge
referencing 0.37.0 pyhcf101f3_0 conda-forge
reportlab 4.5.1 pyhc364b38_0 conda-forge
requests 2.34.2 pyhcf101f3_0 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
rpds-py 0.30.0 py313h843e2db_0 conda-forge
scikit-learn 1.8.0 np2py313h16d504d_1 conda-forge
scikit-mol 0.6.1 pyhd8ed1ab_0 conda-forge
scipy 1.17.1 py313h4b8bb8b_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 py313h54dd161_0 conda-forge
stack_data 0.6.3 pyhd8ed1ab_1 conda-forge
statsmodels 0.14.6 py313h29aa505_0 conda-forge
sympy 1.14.0 pyh2585a3b_106 conda-forge
sysroot_linux-64 2.28 h4ee821c_9 conda-forge
tbb 2022.3.0 h8d10470_1 conda-forge
terminado 0.18.1 pyhc90fa1f_1 conda-forge
threadpoolctl 3.6.0 pyhecae5ae_0 conda-forge
debugpy 1.8.20 py313h5d5ffb9_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
torchmetrics 1.9.0 pyhd8ed1ab_0 conda-forge
tornado 6.5.5 py313h07c4f96_0 conda-forge
tqdm 4.67.3 pyh8f84b5b_0 conda-forge
traitlets 5.15.0 pyhcf101f3_0 conda-forge
typing-extensions 4.15.0 h396c80c_0 conda-forge
typing-inspection 0.4.2 pyhcf101f3_2 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
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.7.0 pyhd8ed1ab_0 conda-forge
validators 0.35.0 pyhd8ed1ab_0 conda-forge
wayland 1.25.0 hd6090a7_0 conda-forge
wcwidth 0.7.0 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
widgetsnbextension 4.0.15 pyhd8ed1ab_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 1.8.3 hb03c661_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 4.1.0 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 py313h54dd161_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
Hello, I was trying to do an RBFE calculation with a 2 ligands transformation.
I tried both the CLI and the python API and it seems like the
quickrunfails with message:I'm running on a NVIDIA H100 and my
conda listlooks like this:Thanks for your help!