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environment.yml
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environment.yml
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ame: Dock-MD-FEP
channels:
#- https://mirrors.ustc.edu.cn/anaconda/pkgs/main
- conda-forge
#- https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
#- https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
- defaults
dependencies:
##- _libgcc_mutex=0.1=conda_forge
#- _openmp_mutex=4.5=2_kmp_llvm
#- alabaster=0.7.12=pyhd3eb1b0_0
#- alsa-lib=1.2.8=h166bdaf_0
#- ambertools=22.0=py38h6177452_1
#- appdirs=1.4.4=pyhd3eb1b0_0
#- argon2-cffi=21.3.0=pyhd3eb1b0_0
#- argon2-cffi-bindings=21.2.0=py38h7f8727e_0
#- arpack=3.7.0=hdefa2d7_2
#- astunparse=1.6.3=py_0
##- attr=2.5.1=h166bdaf_1
##- attrs=22.1.0=py38h06a4308_0
#- backcall=0.2.0=pyhd3eb1b0_0
##- beautifulsoup4=4.11.1=py38h06a4308_0
#- blosc=1.21.3=h6a678d5_0
#- boost-cpp=1.74.0=h75c5d50_8
#- bottleneck=1.3.5=py38h7deecbd_0
#- brotli=1.0.9=h5eee18b_7
#- brotli-bin=1.0.9=h5eee18b_7
#- brotlipy=0.7.0=py38h27cfd23_1003
##- bzip2=1.0.8=h7b6447c_0
##- c-ares=1.18.1=h7f8727e_0
#- ca-certificates=2023.01.10=h06a4308_0
#- cerberus=1.3.4=pyhd3eb1b0_0
#- certifi=2022.12.7=py38h06a4308_0
#- cffi=1.15.1=py38h5eee18b_3
#- cftime=1.5.1.1=py38hce1f21e_0
#- charset-normalizer=2.0.4=pyhd3eb1b0_0
#- clusterutils=0.3.1=pyhd8ed1ab_1
#- colorama=0.4.6=py38h06a4308_0
#- comm=0.1.2=py38h06a4308_0
- conda=23.1.0=py38h06a4308_0
#- conda-package-handling=2.0.2=py38h06a4308_0
#- conda-package-streaming=0.7.0=py38h06a4308_0
#- contourpy=1.0.5=py38hdb19cb5_0
#- cryptography=38.0.4=py38h9ce1e76_0
- cudatoolkit=10.2.89=h8f6ccaa_8
#- curl=7.87.0=h5eee18b_0
#- cycler=0.11.0=pyhd3eb1b0_0
#- cython=0.29.32=py38h6a678d5_0
#- dbus=1.13.18=hb2f20db_0
#- decorator=5.1.1=pyhd3eb1b0_0
#- defusedxml=0.7.1=pyhd3eb1b0_0
#- dill=0.3.6=py38h06a4308_0
#- docopt=0.6.2=py38h06a4308_1
#- docutils=0.18.1=py38h06a4308_3
#- entrypoints=0.4=py38h06a4308_0
#- expat=2.5.0=h27087fc_0
- fftw=3.3.10=nompi_hf0379b8_106
#- flit-core=3.6.0=pyhd3eb1b0_0
#- font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
#- font-ttf-inconsolata=2.001=hcb22688_0
#- font-ttf-source-code-pro=2.030=hd3eb1b0_0
#- font-ttf-ubuntu=0.83=h8b1ccd4_0
#- fontconfig=2.14.2=h14ed4e7_0
#- fonts-anaconda=1=h8fa9717_0
#- fonts-conda-ecosystem=1=hd3eb1b0_0
#- freetype=2.12.1=h4a9f257_0
#- gdbm=1.18=hd4cb3f1_4
#- gettext=0.21.1=h27087fc_0
#- giflib=5.2.1=h5eee18b_1
#- glib=2.74.1=h6239696_1
#- glib-tools=2.74.1=h6239696_1
#- gst-plugins-base=1.21.3=h4243ec0_1
#- gstreamer=1.21.3=h25f0c4b_1
#- gstreamer-orc=0.4.33=h166bdaf_0
#- hdf4=4.2.15=h9772cbc_5
#- hdf5=1.12.2=nompi_h2386368_101
#- icu=70.1=h27087fc_0
#- idna=3.4=py38h06a4308_0
#- imagesize=1.4.1=py38h06a4308_0
#- importlib_resources=5.2.0=pyhd3eb1b0_1
#- ipython_genutils=0.2.0=pyhd3eb1b0_1
#- jack=1.9.22=h11f4161_0
#- jax=0.3.25=py38h06a4308_0
#- jaxlib=0.3.25=py38h6a678d5_1
#- jedi=0.18.1=py38h06a4308_1
#- jinja2=3.1.2=py38h06a4308_0
#- joblib=1.1.1=py38h06a4308_0
#- jpeg=9e=h7f8727e_0
#- jupyter=1.0.0=py38_7
- jupyter_client=7.4.8=py38h06a4308_0
- jupyter_console=6.4.4=py38h06a4308_0
- jupyter_core=5.1.1=py38h06a4308_0
- jupyter_server=1.23.4=py38h06a4308_0
- jupyterlab_pygments=0.1.2=py_0
- jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
#- kiwisolver=1.4.4=py38h6a678d5_0
#- krb5=1.19.4=h568e23c_0
#- lame=3.100=h7b6447c_0
#- lcms2=2.12=h3be6417_0
#- ld_impl_linux-64=2.38=h1181459_1
#- lerc=3.0=h295c915_0
#- libaec=1.0.6=hcb278e6_1
#- libblas=3.9.0=15_linux64_openblas
#- libbrotlicommon=1.0.9=h5eee18b_7
#- libbrotlidec=1.0.9=h5eee18b_7
#- libbrotlienc=1.0.9=h5eee18b_7
#- libcap=2.66=ha37c62d_0
#- libcblas=3.9.0=15_linux64_openblas
#- libclang=15.0.7=default_had23c3d_1
#- libclang13=15.0.7=default_h3e3d535_1
#- libcups=2.3.3=h3e49a29_2
#- libcurl=7.87.0=h91b91d3_0
#- libdb=6.2.32=h6a678d5_1
#- libdeflate=1.8=h7f8727e_5
#- libedit=3.1.20221030=h5eee18b_0
#- libev=4.33=h7f8727e_1
#- libevent=2.1.10=h9b69904_4
#- libffi=3.4.2=h6a678d5_6
#- libflac=1.4.2=h27087fc_0
#- libgcc-ng=12.2.0=h65d4601_19
#- libgcrypt=1.10.1=h166bdaf_0
#- libgfortran-ng=12.2.0=h69a702a_19
#- libgfortran5=12.2.0=h337968e_19
#- libglib=2.74.1=h606061b_1
#- libgomp=12.2.0=h65d4601_19
#- libgpg-error=1.46=h620e276_0
#- libiconv=1.17=h166bdaf_0
#- liblapack=3.9.0=15_linux64_openblas
#- libllvm15=15.0.7=hadd5161_0
#- libnetcdf=4.8.1=nompi_h21705cb_104
#- libnghttp2=1.46.0=hce63b2e_0
#- libogg=1.3.5=h27cfd23_1
#- libopenblas=0.3.20=pthreads_h78a6416_0
#- libopus=1.3.1=h7b6447c_0
#- libpng=1.6.39=h753d276_0
#- libpq=14.5=h72a31a5_3
#- libsndfile=1.2.0=hb75c966_0
#- libsodium=1.0.18=h7b6447c_0
#- libsqlite=3.40.0=h753d276_0
#- libssh2=1.10.0=h8f2d780_0
#- libstdcxx-ng=12.2.0=h46fd767_19
#- libsystemd0=252=h2a991cd_0
#- libtiff=4.5.0=h6a678d5_1
#- libtool=2.4.7=h27087fc_0
#- libudev1=252=h166bdaf_0
#- libuuid=2.32.1=h7f98852_1000
#- libvorbis=1.3.7=h7b6447c_0
#- libwebp=1.2.4=h11a3e52_0
#- libwebp-base=1.2.4=h5eee18b_0
#- libxcb=1.13=h7f98852_1004
#- libxkbcommon=1.0.3=he3ba5ed_0
#- libxml2=2.10.3=h7463322_0
#- libxslt=1.1.37=h873f0b0_0
#- libzip=1.9.2=hc869a4a_1
#- libzlib=1.2.13=h166bdaf_4
#- llvm-openmp=14.0.6=h9e868ea_0
#- lxml=4.9.2=py38h215a2d7_0
#- lz4-c=1.9.4=h6a678d5_0
#- lzo=2.10=h7b6447c_2
#- markupsafe=2.1.1=py38h7f8727e_0
#- matplotlib-base=3.6.2=py38h945d387_0
#- mdtraj=1.9.7=py38hdee7691_4
#- mistune=0.8.4=py38h7b6447c_1000
#- mpg123=1.31.2=hcb278e6_0
- mpi=1.0=mpich
- mpich=4.0.3=h846660c_100
- mpiplus=v0.0.1=pyhd8ed1ab_1003
- multiprocess=0.70.14=py38h06a4308_0
#- munkres=1.1.4=py_0
#- mysql-common=8.0.32=h14678bc_0
#- mysql-libs=8.0.32=h54cf53e_0
#- ncurses=6.4=h6a678d5_0
- netcdf-fortran=4.5.4=nompi_hc402ea5_102
- netcdf4=1.6.2=py38h89d13dc_0
#- nomkl=1.0=h5ca1d4c_0
#- nose=1.3.7=pyhd3eb1b0_1008
#- nspr=4.35=h27087fc_0
#- nss=3.82=he02c5a1_0
#- numexpr=2.8.3=py38h36ff5c2_101
#- numpydoc=1.5.0=py38h06a4308_0
#- ocl-icd=2.3.1=h7f98852_0
#- ocl-icd-system=1.0.0=1
- openmm=8.0.0=py38h83c2b03_0
- openmmtools=0.20.0=py38h497a2fe_1
- openmoltools=0.8.8=pyhd8ed1ab_1
#- openssl=1.1.1s=h7f8727e_0
#- opt_einsum=3.3.0=pyhd3eb1b0_1
- packmol=20.010=h86c2bf4_0
- pandas=1.5.2=py38h417a72b_0
#- pandocfilters=1.5.0=pyhd3eb1b0_0
- parmed=3.4.4=py38h8dc9893_0
#- parso=0.8.3=pyhd3eb1b0_0
#- pcre2=10.40=hc3806b6_0
- pdbfixer=1.8.1=pyh6c4a22f_0
#- perl=5.34.0=h5eee18b_2
#- pexpect=4.8.0=pyhd3eb1b0_3
#- pickleshare=0.7.5=pyhd3eb1b0_1003
- pip=22.3.1=py38h06a4308_0
#- pkgutil-resolve-name=1.3.10=py38h06a4308_0
#- platformdirs=2.5.2=py38h06a4308_0
#- pluggy=1.0.0=py38h06a4308_1
#- ply=3.11=py38_0
#- pooch=1.4.0=pyhd3eb1b0_0
#- prometheus_client=0.14.1=py38h06a4308_0
#- prompt_toolkit=3.0.36=hd3eb1b0_0
#- pthread-stubs=0.3=h0ce48e5_1
#- ptyprocess=0.7.0=pyhd3eb1b0_2
#- pulseaudio=16.1=h4ab2085_1
#- pure_eval=0.2.2=pyhd3eb1b0_0
#- pycosat=0.6.4=py38h5eee18b_0
#- pycparser=2.21=pyhd3eb1b0_0
#- pyopenssl=22.0.0=pyhd3eb1b0_0
#- pyparsing=3.0.9=py38h06a4308_0
- pyqt=5.15.7=py38ha0d8c90_3
#- pyqt5-sip=12.11.0=py38h8dc9893_3
#- pysocks=1.7.1=py38h06a4308_0
#- pytables=3.7.0=py38hf134f34_3
- python=3.8.16=h7a1cb2a_2
#- python-dateutil=2.8.2=pyhd3eb1b0_0
#- python-fastjsonschema=2.16.2=py38h06a4308_0
##- python_abi=3.8=2_cp38
#- pyyaml=6.0=py38h5eee18b_1
#- pyzmq=23.2.0=py38h6a678d5_0
#- qt-main=5.15.6=h7acdfc8_2
#- qtconsole=5.4.0=py38h06a4308_0
#- qtpy=2.2.0=py38h06a4308_0
#- readline=8.2=h5eee18b_0
#- requests=2.28.1=py38h06a4308_0
#- ruamel.yaml=0.17.21=py38h5eee18b_0
#- ruamel.yaml.clib=0.2.6=py38h5eee18b_1
- scikit-learn=1.2.0=py38h6a678d5_0
- scipy=1.10.0=py38h10c12cc_2
- seaborn=0.12.2=py38h06a4308_0
#- send2trash=1.8.0=pyhd3eb1b0_1
#- setuptools=65.6.3=py38h06a4308_0
#- sip=6.7.7=py38h8dc9893_0
#- six=1.16.0=pyhd3eb1b0_1
#- snappy=1.1.9=h295c915_0
#- sniffio=1.2.0=py38h06a4308_1
#- snowballstemmer=2.2.0=pyhd3eb1b0_0
#- soupsieve=2.3.2.post1=py38h06a4308_0
#- sphinx=5.0.2=py38h06a4308_0
#- sphinxcontrib-applehelp=1.0.2=pyhd3eb1b0_0
#- sphinxcontrib-devhelp=1.0.2=pyhd3eb1b0_0
#- sphinxcontrib-htmlhelp=2.0.0=pyhd3eb1b0_0
#- sphinxcontrib-jsmath=1.0.1=pyhd3eb1b0_0
#- sphinxcontrib-qthelp=1.0.3=pyhd3eb1b0_0
#- sphinxcontrib-serializinghtml=1.1.5=pyhd3eb1b0_0
#- sqlite=3.40.1=h5082296_0
#- stack_data=0.2.0=pyhd3eb1b0_0
#- threadpoolctl=2.2.0=pyh0d69192_0
#- ties_md=1.4.1=pyhd8ed1ab_0
#- tk=8.6.12=h1ccaba5_0
#- toml=0.10.2=pyhd3eb1b0_0
#- toolz=0.12.0=py38h06a4308_0
#- tornado=6.2=py38h5eee18b_0
- tqdm=4.64.1=py38h06a4308_0
#- typing-extensions=4.4.0=py38h06a4308_0
#- typing_extensions=4.4.0=py38h06a4308_0
#- urllib3=1.26.14=py38h06a4308_0
#- wcwidth=0.2.5=pyhd3eb1b0_0
#- wheel=0.37.1=pyhd3eb1b0_0
#- xcb-util=0.4.0=h166bdaf_0
#- xcb-util-image=0.4.0=h166bdaf_0
#- xcb-util-keysyms=0.4.0=h166bdaf_0
#- xcb-util-renderutil=0.3.9=h166bdaf_0
#- xcb-util-wm=0.4.1=h166bdaf_0
#- xorg-kbproto=1.0.7=h7f98852_1002
#- xorg-libice=1.0.10=h7f98852_0
#- xorg-libsm=1.2.3=hd9c2040_1000
#- xorg-libx11=1.7.2=h7f98852_0
#- xorg-libxau=1.0.9=h7f98852_0
#- xorg-libxdmcp=1.1.3=h7f98852_0
#- xorg-libxext=1.3.4=h7f98852_1
#- xorg-libxt=1.2.1=h7f98852_2
#- xorg-xextproto=7.3.0=h7f98852_1002
#- xorg-xproto=7.0.31=h27cfd23_1007
#- xz=5.2.10=h5eee18b_1
- yaml=0.2.5=h7b6447c_0
- yank=0.25.2=pyhd8ed1ab_0
#- zeromq=4.3.4=h2531618_0
#- zlib=1.2.13=h166bdaf_4
#- zstandard=0.18.0=py38h5eee18b_0
#- zstd=1.5.2=ha4553b6_0
- pip:
# - absl-py==1.2.0
- amberlite==22.0
# - amberutils==21.0
# - anyio==3.6.1
# - asttokens==2.0.7
- babel==2.10.3
# - bleach==5.0.1
# - cachetools==5.2.0
# - debugpy==1.6.2
# - dimod==0.12.3
# - dwave-networkx==0.8.12
# - executing==0.9.1
# - fastjsonschema==2.16.1
# - fonttools==4.34.4
# - google-auth==2.10.0
# - google-auth-oauthlib==0.4.6
# - grpcio==1.47.0
- importlib-metadata==4.12.0
- importlib-resources==5.9.0
- ipykernel==6.15.1
- ipython==8.4.0
- ipywidgets==7.7.1
# - json5==0.9.9
# - jsonschema==4.9.1
# - jupyter-client==7.3.4
# - jupyter-core==4.11.1
# - jupyter-server==1.18.1
- jupyterlab==3.4.4
# - jupyterlab-language-pack-zh-cn==3.4.post3
- jupyterlab-server==2.15.0
- jupyterlab-widgets==1.1.1
# - markdown==3.4.1
- matplotlib==3.5.2
- matplotlib-inline==0.1.3
- mmpbsa-py==16.0
# - nbclassic==0.4.3
# - nbclient==0.6.6
# - nbconvert==6.5.0
# - nbformat==5.4.0
# - nest-asyncio==1.5.5
- networkx==2.8.8
# - notebook==6.4.12
# - notebook-shim==0.1.0
- numpy==1.23.1
# - oauthlib==3.2.0
# - packaging==21.3
# - packmol-memgen==1.2.3rc0
- pdb4amber==22.0
# - pillow==9.2.0
# - prompt-toolkit==3.0.30
# - protobuf==3.19.4
# - psutil==5.9.1
# - pyasn1==0.4.8
# - pyasn1-modules==0.2.8
# - pygments==2.12.0
- pymbar==3.0.3
# - pyrsistent==0.18.1
- pytraj==2.0.6
# - pytz==2022.1
# - requests-oauthlib==1.3.1
# - rsa==4.9
# - sander==22.0
# - stack-data==0.3.0
# - tabulate==0.8.10
# #- tensorboard==2.9.1
# #- tensorboard-data-server==0.6.1
# #- tensorboard-plugin-wit==1.8.1
# #- terminado==0.15.0
# - ties==20.10
# #- tinycss2==1.1.1
# #- traitlets==5.3.0
# #- webencodings==0.5.1
# #- websocket-client==1.3.3
# #- werkzeug==2.2.2
# #- widgetsnbextension==3.6.1
# #- zipp==3.8.1
prefix: /root/miniconda3