j-wags
commented
4 months ago Thanks for the detailed writeup. I'm unable to reproduce on an ARM mac, but I'm charging my old intel mac to try it there.
Open slochower opened 4 months ago
j-wags
commented
4 months ago Thanks for the detailed writeup. I'm unable to reproduce on an ARM mac, but I'm charging my old intel mac to try it there.
j-wags
commented
4 months ago Some of our CI should be testing on intel macs, and I'm not seeing any issues there, though
j-wags
commented
4 months ago Unable to reproduce with intel mac on OSX 13.2.1, updating to 14 and will report back.
slochower
commented
4 months ago Thanks! And on my end, this is reproducible (not related to this specific molecule/solvent box). Hit the bug trying to use OpenFE stuff (on real ligands) with @mikemhenry and we initially thought it might be related to RDKit, but it does not seem to be. I'm happy to do additional debugging if you need.
j-wags
commented
4 months ago Darn, my intel macbook isn't compatible with OSX 14. If you're up to iterate a bit, could you let me know if this reproduces the issue?
from openff.toolkit import Molecule
mol = Molecule.from_smiles('[H][O][C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[H]')
mol.assign_partial_charges("am1bcc")And if that DOES reproduce the issue, could you run
mol.generate_conformers()
mol.to_file('temp.sdf', file_format='sdf')and in the terminal
antechamber -i molecule.sdf -fi sdf -o charged.mol2 -fo mol2 -pf yes -dr n -c bcc -nc 0.0and let me know what happens?
slochower
commented
4 months ago The small snippet does not reproduce the error.
slochower
commented
4 months ago Oh wait!
I ran it once and it completed without error.
I ran it a second time and it did reproduce the error. Fun.
~/tmp is š¦ v0.1.0 via š v3.12.4 via š
openff-clean took 10s
āÆ python tmp5.py
(openff-clean)
~/tmp is š¦ v0.1.0 via š v3.12.4 via š
openff-clean took 27s
āÆ python tmp5.py
/Users/slochowe/miniforge3/envs/openff-clean/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/Users/slochowe/miniforge3/envs/openff-clean/bin/sqm -O -i sqm.in -o sqm.out".
Traceback (most recent call last):
File "/Users/slochowe/tmp/tmp5.py", line 3, in <module>
mol.assign_partial_charges("am1bcc")
File "/Users/slochowe/miniforge3/envs/openff-clean/lib/python3.12/site-packages/openff/toolkit/topology/molecule.py", line 2677, in assign_partial_charges
toolkit_registry.call(
File "/Users/slochowe/miniforge3/envs/openff-clean/lib/python3.12/site-packages/openff/toolkit/utils/toolkit_registry.py", line 280, in call
raise ValueError(msg)
ValueError: No registered toolkits can provide the capability "assign_partial_charges" for args "()" and kwargs "{'molecule': Molecule with name '' and SMILES '[H][O][C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[H]', 'partial_charge_method': 'am1bcc', 'use_conformers': None, 'strict_n_conformers': False, 'normalize_partial_charges': True, '_cls': <class 'openff.toolkit.topology.molecule.Molecule'>}"
Available toolkits are: [ToolkitWrapper around The RDKit version 2024.03.5, ToolkitWrapper around AmberTools version 23.6, ToolkitWrapper around Built-in Toolkit version None]
ToolkitWrapper around The RDKit version 2024.03.5 <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : partial_charge_method 'am1bcc' is not available from RDKitToolkitWrapper. Available charge methods are {'mmff94': {}, 'gasteiger': {}}
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', 'bcc', '-nc', '0.0']' returned non-zero exit status 1.
ToolkitWrapper around Built-in Toolkit version None <class 'openff.toolkit.utils.exceptions.ChargeMethodUnavailableError'> : Partial charge method "am1bcc"" 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}}
mikemhenry
commented
4 months ago :melting_face:
mikemhenry
commented
4 months ago @slochower can you try this? for i in (seq 10); python tmp5.py; end and lets see how often this happens... (assuming you are using fish shell)
slochower
commented
4 months ago Looks like 5/10. Perfect.
I made a slight modification for i in (seq 10); python tmp5.py && echo "Pass"; end and counted "Pass" five times.
Here's another version:
āŖ for i in (seq 10); python tmp5.py &> /dev/null && echo "Pass $i"; end
Pass 5
Pass 7
Pass 8Okay, so it's Ambertools that is leading to the mess.
āŖ for i in (seq 10); antechamber -i temp.sdf -fi sdf -o charged.mol2 -fo mol2 -pf yes -dr n -c bcc -nc 0.0 &> /dev/null && echo "Pass $i"; end
Pass 2
Pass 4
Pass 5
Pass 8
Pass 10WHen it fails, it's linked to sqm.
And this is what happens when sqm fails.
āÆ cat sqm.in
Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0005,
scfconv=1.d-10, ndiis_attempts=700, qmcharge=0,
/āÆ cat sqm.out
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
QM ATOM VALIDATION: nquant has a value of 0
SANDER BOMB in subroutine validate_qm_atoms
nquant illegal
Need 0 < nquant <= natomThe input file should have the coordinates in it after the / but in cases where it fails, it just ends like above, without coordinates. A correct file would be something like this:
Run semi-empirical minimization
&qmmm
qm_theory='AM1', grms_tol=0.0005,
scfconv=1.d-10, ndiis_attempts=700, qmcharge=0,
/
1 H1 2.5450 1.2970 0.8130
8 O1 2.5880 0.3750 0.4790
6 C1 1.3640 0.0320 -0.1430
1 H2 1.6070 -0.8440 -0.7780
1 H3 1.0220 0.8280 -0.8300
6 C2 0.4040 -0.2880 0.9570
1 H4 0.8200 -1.1770 1.4820
1 H5 0.3520 0.5510 1.6630
6 C3 -0.9630 -0.6780 0.4760
1 H6 -1.6150 -0.8110 1.3650
1 H7 -1.0030 -1.6010 -0.0910
6 C4 -1.6300 0.4120 -0.3350
1 H8 -0.9920 0.7070 -1.1940
1 H9 -1.9350 1.2690 0.3110
1 H10 -2.5640 -0.0710 -0.7400Can you try installing ambertools 22? Hopefully it doesn't cause too much package churn, on my system it looks like this:
- ambertools=22
Package Version Build Channel Size
āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
Install:
āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
+ boost-cpp 1.78.0 h2c5509c_4 conda-forge Cached
+ cython 3.0.10 py310hc6cd4ac_0 conda-forge Cached
+ packmol 20.15.0 hc8b2c43_0 conda-forge 130kB
+ boost 1.78.0 py310hcb52e73_5 conda-forge Cached
Remove:
āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
- libboost 1.84.0 hba137d9_3 conda-forge Cached
- libboost-python 1.84.0 py310he6ccd79_3 conda-forge Cached
Downgrade:
āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
- arpack 3.9.1 nompi_h77f6705_101 conda-forge Cached
+ arpack 3.7.0 hdefa2d7_2 conda-forge Cached
- ambertools 23.6 nompi_py310hcbc9ba0_103 conda-forge Cached
+ ambertools 22.5 py310hd182041_0 conda-forge Cached
- rdkit 2024.03.3 py310h6f17f40_0 conda-forge Cached
+ rdkit 2023.03.3 py310h399bcf7_0 conda-forge Cached
which for our testing purposes isn't too bad, another option would be to keep ambertools 23, but just install an older build, like before mpi support was added for example.
slochower
commented
4 months ago Oof. Couldn't install with the existing 3.12 environment. Stepped back to 3.11, also dependency conflicts. Stepped back to 3.10, also dependency conflicts...
warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
āā ambertools 22** is installable with the potential options
ā āā ambertools 22.0 would require
ā ā āā boost-cpp >=1.74.0,<1.74.1.0a0 with the potential options
ā ā āā boost-cpp 1.74.0 would require
ā ā ā āā icu >=68.1,<69.0a0 , which can be installed;
ā ā āā boost-cpp [1.74.0|1.78.0] would require
ā ā ā āā icu >=70.1,<71.0a0 , which can be installed;
ā ā āā boost-cpp 1.74.0 would require
ā ā ā āā icu >=69.1,<70.0a0 , which can be installed;
ā ā āā boost-cpp 1.74.0 would require
ā ā āā icu >=67.1,<68.0a0 , which can be installed;
ā āā ambertools 22.0 would require
ā ā āā python >=3.7,<3.8.0a0 , which can be installed;
ā āā ambertools [22.0|22.1|...|22.5] would require
ā ā āā python >=3.8,<3.9.0a0 , which can be installed;
ā āā ambertools [22.0|22.1|...|22.5] would require
ā ā āā python >=3.9,<3.10.0a0 , which can be installed;
ā āā ambertools [22.0|22.1|...|22.5] would require
ā āā boost-cpp >=1.78.0,<1.78.1.0a0 with the potential options
ā āā boost-cpp [1.74.0|1.78.0], which can be installed (as previously explained);
ā āā boost-cpp 1.78.0 would require
ā ā āā icu >=73.2,<74.0a0 , which conflicts with any installable versions previously reported;
ā ā āā libboost <0 , which can be installed;
ā āā boost-cpp 1.78.0 would require
ā āā icu >=72.1,<73.0a0 , which can be installed;
āā libboost is installable with the potential options
ā āā libboost [1.84.0|1.85.0] would require
ā ā āā icu >=75.1,<76.0a0 , which conflicts with any installable versions previously reported;
ā āā libboost 1.84.0 would require
ā ā āā boost-cpp 1.84.0* , which conflicts with any installable versions previously reported;
ā ā āā icu >=73.2,<74.0a0 , which conflicts with any installable versions previously reported;
ā āā libboost 1.82.0 would require
ā ā āā icu >=72.1,<73.0a0 , which can be installed;
ā āā libboost 1.82.0 would require
ā ā āā boost-cpp 1.82.0* , which conflicts with any installable versions previously reported;
ā āā libboost 1.83.0 would require
ā ā āā boost-cpp 1.83.0* , which conflicts with any installable versions previously reported;
ā āā libboost 1.85.0 would require
ā ā āā boost-cpp 1.85.0* , which conflicts with any installable versions previously reported;
ā āā libboost [1.65.1|1.67.0|1.71.0|1.73.0] would require
ā ā āā icu >=58.2,<59.0a0 , which can be installed;
ā āā libboost 1.82.0 conflicts with any installable versions previously reported;
āā librdkit is not installable because it requires
āā libboost >=1.84.0,<1.85.0a0 , which cannot be installed (as previously explained).sigh, how about ambertools=23.3
slochower
commented
4 months ago Sadly not. Looks like libboost is the culprit, at least when trying in the original environment.
āŖ mamba install ambertools=23.3 (openff-clean)
Looking for: ['ambertools=23.3']
conda-forge/osx-64 Using cache
conda-forge/noarch Using cache
pkgs/main/noarch No change
pkgs/r/osx-64 No change
pkgs/r/noarch No change
pkgs/main/osx-64 No change
Pinned packages:
- python 3.12.*
warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
āā ambertools 23.3** is installable with the potential options
ā āā ambertools 23.3 would require
ā ā āā libboost >=1.82.0,<1.83.0a0 with the potential options
ā ā āā libboost 1.82.0 would require
ā ā ā āā icu >=72.1,<73.0a0 , which can be installed;
ā ā āā libboost 1.82.0 would require
ā ā ā āā icu >=73.2,<74.0a0 , which can be installed;
ā ā āā libboost 1.82.0 would require
ā ā āā icu >=73.1,<74.0a0 , which can be installed;
ā āā ambertools 23.3 would require
ā ā āā python >=3.10,<3.11.0a0 , which can be installed;
ā āā ambertools 23.3 would require
ā ā āā python >=3.11,<3.12.0a0 , which can be installed;
ā āā ambertools 23.3 would require
ā ā āā python >=3.8,<3.9.0a0 , which can be installed;
ā āā ambertools 23.3 would require
ā āā python >=3.9,<3.10.0a0 , which can be installed;
āā librdkit is not installable because it requires
āā libboost >=1.84.0,<1.85.0a0 but there are no viable options
āā libboost 1.84.0 would require
ā āā icu >=75.1,<76.0a0 , which conflicts with any installable versions previously reported;
āā libboost 1.84.0 conflicts with any installable versions previously reported.Is that making a fresh env? Using some hacks (I am on linux) it looks like it should solve on osx-arm64 CONDA_SUBDIR="osx-arm64" micromamba create -n foooooobar --dry-run -c conda-forge ambertools=23.3 "openff-toolkit=0.16.*" BUT I know sometimes when you have an env, the solver can get stuck trying to figure things out but a fresh one can help it out.
slochower
commented
4 months ago Good point. Although 23.3 is still flaky. I can step back to 22 in a new environment.
āŖ for i in (seq 10); antechamber -i temp.sdf -fi sdf -o charged.mol2 -fo mol2 -pf yes -dr n -c bcc -nc 0.0 &> /dev/null && echo "Pass $i"; end
Pass 1
Pass 3
Pass 4
Pass 5
Pass 6
Pass 7Here's ambertools=22 ...
āŖ for i in (seq 10); antechamber -i temp.sdf -fi sdf -o charged.mol2 -fo mol2 -pf yes -dr n -c bcc -nc 0.0 &> /dev/null && echo "Pass $i"; end
Pass 2
Pass 3
Pass 4
Pass 5
Pass 7
Pass 8š°
mikemhenry
commented
4 months ago okay one more idea,
antechamber -i molecule.sdf -fi sdf -o charged.mol2 -fo mol2 -pf yes -dr n -c bcc -nc 0.0 -ek
see if adding the -ek arg helps at all
slochower
commented
4 months ago I think that needs something after it?
mikemhenry
commented
4 months ago You are correct! -ek pseudo_diag=0 We can use -ek to pass in arguments to sqm, I've seen some weird things where diagonalization options/methods causes sqm to not be deterministic -- this is a bit of a rabbit hole since even if we figure out some collection of arguments that makes sqm work consistently, it is unclear if we can get those options upstreamed into the toolkit.
Another option to pass in is diag_routine=3, so try -ek "pseudo_diag=0, diag_routine=3" and see if that gets us 10 passes.
slochower
commented
4 months ago āŖ antechamber -i temp.sdf -fi sdf -o charged.mol2 -fo mol2 -pf yes -dr n -c bcc -nc 0.0 -ek pseudo_diag=0
Welcome to antechamber 22.0: molecular input file processor.
Info: The atom type is set to gaff; the options available to the -at flag are
gaff, gaff2, amber, bcc, and sybyl.
Info: Total number of electrons: 0; net charge: 0
Running: /Users/slochowe/miniforge3/envs/foo2/bin/sqm -O -i sqm.in -o sqm.out
/Users/slochowe/miniforge3/envs/foo2/bin/wrapped_progs/antechamber: Fatal Error!
Cannot properly run "/Users/slochowe/miniforge3/envs/foo2/bin/sqm -O -i sqm.in -o sqm.out".I don't think this is a problem inside sqm but rather -- the input file is not being written correctly:
āŖ bat sqm.in (foo2)
āāāāāāāā¬āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
ā File: sqm.in
āāāāāāāā¼āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
1 ā Run semi-empirical minimization
2 ā &qmmm
3 ā pseudo_diag=0 qmcharge=0,
4 ā /
5 ā
āāāāāāāā“āāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāāā
mattwthompson
commented
1 month ago IIUC, the toolkit doesn't actually write that file, so something before that step is failing?
I can't reproduce this behavior this morning using cuda_None_nompi_py312hc98840c_105
Describe the bug In a new, clean OpenFF environment on an x86-64 Mac (14.4.1), partial charge methods fail. This is either from
antechamberor possiblysqmand probably related to issues that I've seen @mattwthompson talking about with the Amber folks.For this test script:
I'm seeing:
The test cases also fail.
To Reproduce
conda create --name openff-cleanmamba install -c conda-forge openff-toolkittmp.pypython tmp.pyOutput
`conda list`
``` āÆ conda list # packages in environment at /Users/slochowe/miniforge3/envs/openff-clean: # # Name Version Build Channel ambertools 23.6 cuda_None_nompi_py312hc98840c_105 conda-forge amberutils 21.0 pypi_0 pypi annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge anyio 4.4.0 pyhd8ed1ab_0 conda-forge appnope 0.1.4 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py312h104f124_4 conda-forge arpack 3.9.1 nompi_hf81eadf_101 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blosc 1.21.6 h7d75f6d_0 conda-forge brotli 1.1.0 h0dc2134_1 conda-forge brotli-bin 1.1.0 h0dc2134_1 conda-forge brotli-python 1.1.0 py312heafc425_1 conda-forge bson 0.5.9 py_0 conda-forge bzip2 1.0.8 hfdf4475_7 conda-forge c-ares 1.32.3 h51dda26_0 conda-forge c-blosc2 2.15.0 hb9356d3_1 conda-forge ca-certificates 2024.7.4 h8857fd0_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.4.0 pyhd8ed1ab_0 conda-forge cairo 1.18.0 h37bd5c4_3 conda-forge certifi 2024.7.4 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py312h38bf5a0_0 conda-forge chardet 5.2.0 py312hb401068_1 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py312h9230928_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge debugpy 1.8.2 py312h28f332c_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge edgembar 0.2 pypi_0 pypi entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h73e2aa4_0 conda-forge fftw 3.3.10 nompi_h292e606_110 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_2 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 4.53.1 py312hbd25219_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h60636b9_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge greenlet 3.0.3 py312hede676d_0 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge hdf4 4.2.15 h8138101_7 conda-forge hdf5 1.14.3 nompi_h687a608_105 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge httpcore 1.0.5 pyhd8ed1ab_0 conda-forge httpx 0.27.0 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 75.1 h120a0e1_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 8.2.0 pyha770c72_0 conda-forge importlib_metadata 8.2.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge ipykernel 6.29.5 pyh57ce528_0 conda-forge ipython 8.26.0 pyh707e725_0 conda-forge ipywidgets 8.1.3 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pyhd8ed1ab_0 conda-forge json5 0.9.25 pyhd8ed1ab_0 conda-forge jsonpointer 3.0.0 py312hb401068_0 conda-forge jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py312hb401068_0 conda-forge jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge jupyterlab 4.2.4 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge jupyterlab_server 2.27.3 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python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.12 4_cp312 conda-forge pytraj 2.0.6 pypi_0 pypi pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py312h104f124_1 conda-forge pyzmq 26.0.3 py312ha04878a_0 conda-forge qhull 2020.2 h3c5361c_5 conda-forge rdkit 2024.03.5 py312hcfd6466_1 conda-forge readline 8.2 h9e318b2_1 conda-forge referencing 0.35.1 pyhd8ed1ab_0 conda-forge reportlab 4.2.2 py312hbd25219_0 conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge rpds-py 0.19.1 py312ha47ea1c_0 conda-forge sander 22.0 pypi_0 pypi scipy 1.14.0 py312hb9702fa_1 conda-forge send2trash 1.8.3 pyh31c8845_0 conda-forge setuptools 71.0.4 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge snappy 1.2.1 he1e6707_0 conda-forge sniffio 1.3.1 pyhd8ed1ab_0 conda-forge soupsieve 2.5 pyhd8ed1ab_1 conda-forge sqlalchemy 2.0.31 py312hbd25219_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge terminado 0.18.1 pyh31c8845_0 conda-forge tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge tk 8.6.13 h1abcd95_1 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.4.1 py312hbd25219_0 conda-forge tqdm 4.66.4 pyhd8ed1ab_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge typing-extensions 4.12.2 hd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 2.2.2 pyhd8ed1ab_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webcolors 24.6.0 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 4.0.11 pyhd8ed1ab_0 conda-forge xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h35c211d_1002 conda-forge xorg-libice 1.1.1 h0dc2134_0 conda-forge xorg-libsm 1.2.4 h0dc2134_0 conda-forge xorg-libx11 1.8.9 h7022169_1 conda-forge xorg-libxau 1.0.11 h0dc2134_0 conda-forge xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge xorg-libxext 1.3.4 hb7f2c08_2 conda-forge xorg-libxt 1.3.0 h0dc2134_1 conda-forge xorg-xextproto 7.3.0 hb7f2c08_1003 conda-forge xorg-xproto 7.0.31 h35c211d_1007 conda-forge xz 5.2.6 h775f41a_0 conda-forge yaml 0.2.5 h0d85af4_2 conda-forge zeromq 4.3.5 hde137ed_4 conda-forge zipp 3.19.2 pyhd8ed1ab_0 conda-forge zlib 1.3.1 h87427d6_1 conda-forge zlib-ng 2.2.1 hf036a51_0 conda-forge zstd 1.5.6 h915ae27_0 conda-forge ```CC @mikemhenry