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openforcefield / openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io
http://openforcefield.org
MIT License
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Error calling ambertools #1900

Closed velocirraptor23 closed 1 day ago

velocirraptor23 commented 4 days ago

Hi,

I installed a fressh conda enviroment with openff-toolkit along with penff-nagl. However when I check if I had correctly installed everything I got this error:

from openff.toolkit import GLOBAL_TOOLKIT_REGISTRY Traceback (most recent call last): File "", line 1, in File "", line 1412, in _handle_fromlist File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/toolkit/init.py", line 81, in getattr mod = importlib.import_module(obj_mod) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/importlib/init.py", line 90, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/toolkit/utils/init.py", line 9, in from openff.toolkit.utils.toolkits import ( File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/toolkit/utils/toolkits.py", line 102, in GLOBAL_TOOLKIT_REGISTRY = ToolkitRegistry( ^^^^^^^^^^^^^^^^ File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/toolkit/utils/toolkit_registry.py", line 127, in init self.register_toolkit( File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/toolkit/utils/toolkit_registry.py", line 314, in register_toolkit _toolkit_wrapper = toolkit_wrapper() ^^^^^^^^^^^^^^^^^ File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/toolkit/utils/ambertools_wrapper.py", line 73, in init self._toolkit_version = get_ambertools_version() ^^^^^^^^^^^^^^^^^^^^^^^^ File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/utilities/provenance.py", line 42, in get_ambertools_version return _get_conda_list_package_versions().get("ambertools", None) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cluster/ddu/cmmartinez001/miniconda3/envs/OFF_z/lib/python3.12/site-packages/openff/utilities/provenance.py", line 33, in _get_conda_list_package_versions package_name, packageversion, * = output_line.split() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ValueError: not enough values to unpack (expected at least 2, got 1)

No sure what this error means really. openMM is working fine. Any help would be highly appreciated. Installation command: mamba create -n OFF_z -c conda-forge openff-toolkit cudatoolkit=11.8 openff-nagl=0.3.8 Packages in the enviroment: _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge absl-py 2.1.0 pyhd8ed1ab_0 conda-forge ambertools 23.6 cuda_None_nompi_py312h41aabf6_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 argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py312h98912ed_4 conda-forge arpack 3.9.1 nompi_h77f6705_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 aws-c-auth 0.7.22 hf36ad8f_6 conda-forge aws-c-cal 0.6.15 h816f305_1 conda-forge aws-c-common 0.9.23 h4ab18f5_0 conda-forge aws-c-compression 0.2.18 he027950_7 conda-forge aws-c-event-stream 0.4.2 hb72ac1a_14 conda-forge aws-c-http 0.8.2 h75ac8c9_3 conda-forge aws-c-io 0.14.9 hd3d3696_3 conda-forge aws-c-mqtt 0.10.4 hb0abfc5_7 conda-forge aws-c-s3 0.5.10 h44b787d_4 conda-forge aws-c-sdkutils 0.1.16 he027950_3 conda-forge aws-checksums 0.1.18 he027950_7 conda-forge aws-crt-cpp 0.26.12 he940a02_1 conda-forge aws-sdk-cpp 1.11.329 h0f5bab0_6 conda-forge azure-core-cpp 1.12.0 h830ed8b_0 conda-forge azure-identity-cpp 1.8.0 hdb0d106_1 conda-forge azure-storage-blobs-cpp 12.11.0 ha67cba7_1 conda-forge azure-storage-common-cpp 12.6.0 he3f277c_1 conda-forge azure-storage-files-datalake-cpp 12.10.0 h29b5301_1 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge blas 1.0 openblas conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blosc 1.21.6 hef167b5_0 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py312h30efb56_1 conda-forge bson 0.5.9 py_0 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.28.1 hd590300_0 conda-forge c-blosc2 2.15.0 h6d6b9e4_1 conda-forge ca-certificates 2024.6.2 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.3 pyhd8ed1ab_0 conda-forge cairo 1.18.0 hbb29018_2 conda-forge certifi 2024.6.2 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py312hf06ca03_0 conda-forge chardet 5.2.0 py312h7900ff3_1 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge click-option-group 0.5.6 pyhd8ed1ab_0 conda-forge cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py312h8572e83_0 conda-forge cuda-version 11.8 h70ddcb2_3 conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge cudnn 8.9.7.29 hbc23b4c_3 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cytoolz 0.12.3 py312h98912ed_0 conda-forge dask-core 2024.6.2 pyhd8ed1ab_0 conda-forge dask-jobqueue 0.8.5 pyhd8ed1ab_0 conda-forge debugpy 1.8.2 py312h7070661_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dgl 2.1.0 cuda118py312hd2553cf_1 conda-forge distributed 2024.6.2 pyhd8ed1ab_0 conda-forge dm-tree 0.1.8 py312h72fbbdf_4 conda-forge edgembar 0.2 pypi_0 pypi entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge fftw 3.3.10 nompi_hf1063bd_110 conda-forge filelock 3.15.4 pyhd8ed1ab_0 conda-forge flatbuffers 24.3.25 h59595ed_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.0 py312h9a8786e_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge fsspec 2024.6.1 pyhff2d567_0 conda-forge gast 0.5.5 pyhd8ed1ab_0 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge giflib 5.2.2 hd590300_0 conda-forge glog 0.7.1 hbabe93e_0 conda-forge gmp 6.3.0 hac33072_2 conda-forge gmpy2 2.1.5 py312h1d5cde6_1 conda-forge google-pasta 0.2.0 pyh8c360ce_0 conda-forge greenlet 3.0.3 py312h30efb56_0 conda-forge grpcio 1.62.2 py312hb06c811_0 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge h5py 3.11.0 nompi_py312hb7ab980_102 conda-forge hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_hdf9ad27_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 73.2 h59595ed_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 8.0.0 pyha770c72_0 conda-forge importlib_metadata 8.0.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge ipykernel 6.29.4 pyh3099207_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 py312h7900ff3_0 conda-forge jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_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 py312h7900ff3_0 conda-forge jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.14.1 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge jupyterlab 4.2.3 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge jupyterlab_server 2.27.2 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 3.0.11 pyhd8ed1ab_0 conda-forge keras 3.1.0 pyhd8ed1ab_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py312h8572e83_1 conda-forge krb5 1.21.3 h659f571_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20240116.2 cxx17_h59595ed_0 conda-forge libaec 1.1.3 h59595ed_0 conda-forge libarrow 16.1.0 h4a673ee_10_cpu conda-forge libarrow-acero 16.1.0 hac33072_10_cpu conda-forge libarrow-dataset 16.1.0 hac33072_10_cpu conda-forge libarrow-substrait 16.1.0 h7e0c224_10_cpu conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libboost 1.84.0 hba137d9_3 conda-forge libboost-python 1.84.0 py312h389efb2_3 conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 8.8.0 hca28451_1 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 14.1.0 h77fa898_0 conda-forge libgfortran-ng 14.1.0 h69a702a_0 conda-forge libgfortran5 14.1.0 hc5f4f2c_0 conda-forge libglib 2.80.2 h8a4344b_1 conda-forge libgomp 14.1.0 h77fa898_0 conda-forge libgoogle-cloud 2.25.0 h2736e30_0 conda-forge libgoogle-cloud-storage 2.25.0 h3d9a0c8_0 conda-forge libgrpc 1.62.2 h15f2491_0 conda-forge libhwloc 2.10.0 default_h5622ce7_1001 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge liblapacke 3.9.0 22_linux64_openblas conda-forge libmagma 2.7.2 h09b5827_2 conda-forge libmagma_sparse 2.7.2 h09b5827_3 conda-forge libnetcdf 4.9.2 nompi_h135f659_114 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libparquet 16.1.0 h6a7eafb_10_cpu conda-forge libpng 1.6.43 h2797004_0 conda-forge libprotobuf 4.25.3 h08a7969_0 conda-forge libre2-11 2023.09.01 h5a48ba9_2 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge libthrift 0.19.0 hb90f79a_1 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libtorch 2.3.1 cuda118_h7aef8b2_300 conda-forge liburing 2.6 h297d8ca_0 conda-forge libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.48.0 hd590300_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.16 hd590300_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.12.7 hc051c1a_1 conda-forge libzip 1.10.1 h2629f0a_3 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge lightning-utilities 0.11.3.post0 pyhd8ed1ab_0 conda-forge llvm-openmp 18.1.8 hf5423f3_0 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 hd590300_1001 conda-forge markdown 3.6 pyhd8ed1ab_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.5 py312h98912ed_0 conda-forge matplotlib-base 3.8.4 py312h20ab3a6_2 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mda-xdrlib 0.2.0 pyhd8ed1ab_0 conda-forge mdtraj 1.10.0 py312h0b8b674_0 conda-forge mdurl 0.1.2 pyhd8ed1ab_0 conda-forge metis 5.1.1 h59595ed_2 conda-forge mistune 3.0.2 pyhd8ed1ab_0 conda-forge mkl 2023.2.0 h84fe81f_50496 conda-forge ml_dtypes 0.3.2 py312hfb8ada1_0 conda-forge mmpbsa-py 16.0 pypi_0 pypi mpc 1.3.1 hfe3b2da_0 conda-forge mpfr 4.2.1 h9458935_1 conda-forge mpmath 1.3.0 pyhd8ed1ab_0 conda-forge msgpack-python 1.0.8 py312h2492b07_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge namex 0.0.8 pyhd8ed1ab_0 conda-forge nbclient 0.10.0 pyhd8ed1ab_0 conda-forge nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge nbformat 5.10.4 pyhd8ed1ab_0 conda-forge nccl 2.22.3.1 hee583db_0 conda-forge ncurses 6.5 h59595ed_0 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge netcdf-fortran 4.6.1 nompi_h228c76a_104 conda-forge networkx 3.3 pyhd8ed1ab_1 conda-forge nomkl 3.0 0 anaconda notebook 7.2.1 pyhd8ed1ab_0 conda-forge notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge numexpr 2.10.0 py312hf412c99_100 conda-forge numpy 1.26.4 py312heda63a1_0 conda-forge ocl-icd 2.3.2 hd590300_1 conda-forge ocl-icd-system 1.0.0 1 conda-forge openblas 0.3.27 pthreads_h7a3da1a_0 conda-forge openff-amber-ff-ports 0.0.4 pyhca7485f_0 conda-forge openff-forcefields 2024.04.0 pyhca7485f_0 conda-forge openff-interchange 0.3.27 pyhd8ed1ab_0 conda-forge openff-interchange-base 0.3.27 pyhd8ed1ab_0 conda-forge openff-models 0.1.2 pyhca7485f_0 conda-forge openff-nagl 0.3.8 pyhd8ed1ab_0 conda-forge openff-nagl-base 0.3.8 pyhd8ed1ab_0 conda-forge openff-nagl-models 0.2.0 pyhd8ed1ab_0 conda-forge openff-recharge 0.5.2 pyhd8ed1ab_0 conda-forge openff-toolkit 0.16.1 pyhd8ed1ab_0 conda-forge openff-toolkit-base 0.16.1 pyhd8ed1ab_0 conda-forge openff-units 0.2.2 pyhca7485f_0 conda-forge openff-utilities 0.1.12 pyhd8ed1ab_0 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openmm 8.1.1 py312hce710af_1 conda-forge openssl 3.3.1 h4ab18f5_1 conda-forge opt_einsum 3.3.0 pyhc1e730c_2 conda-forge orc 2.0.1 h17fec99_1 conda-forge overrides 7.7.0 pyhd8ed1ab_0 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge packmol-memgen 2024.2.9 pypi_0 pypi pandas 2.2.2 py312h1d6d2e6_1 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge panedr 0.8.0 pyhd8ed1ab_0 conda-forge parmed 4.2.2 py312h30efb56_1 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge partd 1.4.2 pyhd8ed1ab_0 conda-forge pcre2 10.44 h0f59acf_0 conda-forge pdb4amber 22.0 pypi_0 pypi perl 5.32.1 7_hd590300_perl5 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.3.0 py312h287a98d_1 conda-forge pint 0.23 pyhd8ed1ab_1 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.47 pyha770c72_0 conda-forge protobuf 4.25.3 py312h72fbbdf_0 conda-forge psutil 6.0.0 py312h9a8786e_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge pyarrow 16.1.0 py312h9cebb41_4 conda-forge pyarrow-core 16.1.0 py312h70856f0_4_cpu conda-forge pycairo 1.26.1 py312h3bc4990_0 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pydantic 2.7.4 pyhd8ed1ab_0 conda-forge pydantic-core 2.18.4 py312h4413252_0 conda-forge pyedr 0.8.0 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pymsmt 22.0 pypi_0 pypi pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytables 3.9.2 py312hf20fedc_3 conda-forge python 3.12.4 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BW,

Cesar

velocirraptor23 commented 4 days ago

Fixed. I just commented the lines when it is calling mamba. I kept conda only in provenance.py.

BW,

Cesar

j-wags commented 3 days ago

Thanks for writing in. This is a new error for me. Could you paste the output of running conda info and mamba info?

velocirraptor23 commented 2 days ago

I reinstalled everything. Seems to work fine. Now with python 3.11. Not sure what was that. I had already deleted the enviroment before your comment. Perhaps the python version? Thanks a lot Jeff.

BW,

Cesar

j-wags commented 1 day ago

Thanks for the follow up. My guess about what happened is that you had two miniconda directories on your computer, where "miniconda 1" had mamba in the base env, but "miniconda 2" didn't. Your terminal had activated "miniconda 1" first, then "miniconda 2". So you were intending to be in some env in "miniconda 2", but when the process called "mamba list ...", it resolved to the "mamba" in the base env of "miniconda 1", which didn't have AmberTools (since that was only installed in some env in "miniconda 2").

Anyway, that's just my top suspicion, it might have been something else. Either way I'm glad you got it working :-)