andriy@andriy-Precision-Tower-5810:~/amber24_src/build$ make install [ 0%] Built target ucpp [ 0%] Built target simd_support [ 2%] Built target fftw_api [ 3%] Built target dft [ 3%] Built target dft_scalar [ 4%] Built target dft_scalar_codelets [ 8%] Built target dft_sse2_codelets [ 8%] Built target rdft [ 8%] Built target rdft_scalar [ 10%] Built target rdft_scalar_r2cb [ 12%] Built target rdft_scalar_r2cf [ 12%] Built target rdft_scalar_r2r [ 13%] Built target rdft_sse2_codelets [ 14%] Built target fftw_kernel [ 14%] Built target reodft [ 14%] Built target fftw [ 15%] Built target libfftw_bench [ 15%] Built target fftw_benchmark_common_obj [ 15%] Built target fftw_benchmark [ 15%] Built target fftw_wisdom [ 15%] Built target dispatch [ 16%] Built target netcdf3 [ 16%] Built target netcdf [ 16%] Built target ncgen [ 16%] Built target ncgen3 [ 17%] Built target ncdump [ 17%] Built target nccopy [ 17%] Built target netcdff [ 17%] Built target xblas_build [ 19%] Built target blas [ 25%] Built target lapack [ 26%] Built target arpack [ 26%] Built target PerlMol [ 26%] Built target boost_build [ 26%] Built target tng_io [ 26%] Built target generate-cpp [ 26%] Built target generate-fortran [ 27%] Built target nlopt [ 27%] Built target amber_common [ 28%] Built target rism [ 28%] Built target sff_rism_interface [ 28%] Built target sff_lex [ 28%] Built target dsarpack_obj [ 28%] Built target sff [ 29%] Built target gbnsr6 [ 29%] Built target cifparse [ 30%] Built target addles [ 30%] Built target libcew [ 31%] Built target sqm_common [ 31%] Built target libsqm [ 32%] Built target libpbsa [ 32%] Built target sff_fortran [ 32%] Built target sander_rism_interface [ 36%] Built target xc [ 36%] Built target octree [ 39%] Built target libquick [ 44%] Built target sander_base_obj [ 46%] Built target sebomd [ 46%] Built target emil [ 46%] Built target kmmd [ 46%] Built target pbsa_sander [ 46%] Built target sander [ 51%] Built target sander.LES [ 51%] Built target ambmask [ 56%] Built target libsander [ 61%] Built target libsanderles [ 61%] Built target makeDIST_RST [ 61%] Built target makeANG_RST [ 61%] Built target nef_to_RST [ 63%] Built target nmode [ 63%] Built target antechamber_eprintf_obj [ 63%] Built target am1bcc [ 63%] Built target atomtype [ 63%] Built target espgen [ 63%] Built target parmcal [ 63%] Built target parmchk2 [ 63%] Built target prepgen [ 63%] Built target residuegen [ 63%] Built target respgen [ 63%] Built target match [ 64%] Built target match_atomname [ 64%] Built target antechamber [ 64%] Built target bondtype [ 64%] Built target test-penalties [ 64%] Built target test-int-part [ 65%] Built target test-combination [ 66%] Built target sqm [ 67%] Built target pdb++ [ 67%] Built target toolclasses [ 67%] Built target reduce [ 67%] Built target ndiff [ 69%] Built target gem.pmemd [ 69%] Built target add_pdb [ 69%] Built target add_xray [ 79%] Built target cpptraj_common_obj [ 79%] Built target xdrfile [ 80%] Built target cpptraj [ 80%] Built target libcpptraj [ 81%] Built target cpptraj_core [ 81%] Built target cpptraj_file [ 81%] Built target cpptraj_traj [ 82%] Built target cpptraj_parm [ 82%] Built target ambpdb [ 84%] Built target pbsa [ 84%] Built target simplepbsa [ 84%] Built target hcp_getpdb [ 84%] Built target rism3d.snglpnt [ 84%] Built target rism1d [ 84%] Built target elsize [ 85%] Built target resp [ 85%] Built target gwh [ 85%] Built target tinker_to_amber [ 86%] Built target mdgx_common_obj [ 86%] Built target mdgx [ 86%] Built target libmdgx [ 86%] Built target Xtal [ 86%] Built target AddToBox [ 86%] Built target ChBox [ 86%] Built target PropPDB [ 86%] Built target UnitCell [ 86%] Built target saxs_common_obj [ 86%] Built target saxs_rism [ 86%] Built target saxs_md [ 86%] Built target libsaxs_rism [ 86%] Built target libsaxs_md [ 86%] Built target make_crd_hg [ 86%] Built target nabc [ 86%] Built target mm_pbsa_nabnmode [ 87%] Built target paramfit [ 87%] Built target draw_membrane2 [ 87%] Built target cphstats [ 87%] Built target cestats [ 88%] Built target quick [ 88%] Built target test-api [ 88%] Built target nfe-umbrella-slice [ 88%] Built target leap_common_obj [ 88%] Built target leap_general_obj [ 89%] Built target leap_hierarchy_obj [ 90%] Built target utilMakeHelp [ 90%] Built target leap_leap_obj [ 90%] Built target leap_terminal_obj [ 90%] Built target teLeap [ 90%] Built target mmpbsa_py_energy [ 90%] Built target mmpbsa_py_nabnmode [ 90%] Building pysander native library Copying sander extension source to sanderles... running build running build_py copying sanderles/__init__.py -> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles running build_ext building 'sanderles.pysander' extension gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -DLES -I/home/andriy/amber24_src/AmberTools/src/include -I/home/andriy/amber24_src/AmberTools/src/sander -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c sanderles/src/pysandermodule.c -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o In file included from sanderles/src/pysandermodule.c:16: /home/andriy/amber24_src/AmberTools/src/sander/sander.h: In function ‘pysander_setup’: /home/andriy/amber24_src/AmberTools/src/sander/sander.h:342:5: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 342 | strncpy(prmtop, prmname, __MAX_FN_LEN); | ^ gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o -L/home/andriy/amber24_src/build/AmberTools/src/sander -L/home/andriy/amber24_src/build/AmberTools/src/sander -lsanderles -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/pysander.cpython-311-x86_64-linux-gnu.so [ 90%] Built target pysander [ 90%] Building pytraj native library sys.argv ['setup.py', 'build', '-b', '/home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build', '--disable-openmp'] Original compiler envs CXX = /usr/bin/g++ CC = /usr/bin/gcc COMPILER = use_pip = False, cpptraj_home = compile_c_extension = True 2.0.6 use_prebuilt_cythonized_files = False pytraj is inside AMBERHOME using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++ using CC=/usr/bin/gcc, CXX=/usr/bin/g++ Final compiler envs CXX = /usr/bin/g++ CC = /usr/bin/gcc COMPILER = install = True set rpath to /home/andriy/amber24_src/build/AmberTools/src/cpptraj/src /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/dist.py:476: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py copying pytraj/version.py -> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj running build_ext [ 90%] Built target pytraj [ 90%] Built target memembed [ 91%] Built target packmol [ 91%] Built target immers [ 91%] Built target metatwist [ 92%] Built target edgembar [ 93%] Built target ndfes [ 93%] Built target ndfes-path [ 93%] Built target pmemd_xray_contracts [ 94%] Built target xray_fft_interface [ 94%] Built target pmemd_xray_cpu [ 97%] Built target pmemd [100%] Built target pmemd.decomp Install the project... -- Install configuration: "RELEASE" -- Installing: /home/andriy/amber24/miniconda/bin/xzmore -- Installing: /home/andriy/amber24/miniconda/bin/ipython -- Installing: /home/andriy/amber24/miniconda/bin/mrcfile-validate -- Installing: /home/andriy/amber24/miniconda/bin/xzgrep -- Installing: /home/andriy/amber24/miniconda/bin/pyftsubset -- Installing: /home/andriy/amber24/miniconda/bin/jupyter -- Installing: /home/andriy/amber24/miniconda/bin/icu-config -- Installing: /home/andriy/amber24/miniconda/bin/pyftmerge -- Installing: /home/andriy/amber24/miniconda/bin/pdb2pqr -- Installing: /home/andriy/amber24/miniconda/bin/send2trash -- Installing: /home/andriy/amber24/miniconda/bin/deactivate -- Installing: /home/andriy/amber24/miniconda/bin/conda-env -- Installing: /home/andriy/amber24/miniconda/bin/conda-skeleton -- Installing: /home/andriy/amber24/miniconda/bin/conda-debug -- Installing: /home/andriy/amber24/miniconda/bin/jlpm -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-events -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-dejavu -- Installing: /home/andriy/amber24/miniconda/bin/2to3-3.11 -- Installing: /home/andriy/amber24/miniconda/bin/conda-inspect -- Installing: /home/andriy/amber24/miniconda/bin/idle3.11 -- Installing: /home/andriy/amber24/miniconda/bin/xzdiff -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-run -- Installing: /home/andriy/amber24/miniconda/bin/httpx -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-kernelspec -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-migrate -- Installing: /home/andriy/amber24/miniconda/bin/cygdb -- Installing: /home/andriy/amber24/miniconda/bin/normalizer -- Installing: /home/andriy/amber24/miniconda/bin/mrcfile-header -- Installing: /home/andriy/amber24/miniconda/bin/ipython3 -- Installing: /home/andriy/amber24/miniconda/bin/wsdump -- Installing: /home/andriy/amber24/miniconda/bin/pydoc3.11 -- Installing: /home/andriy/amber24/miniconda/bin/conda-content-trust -- Installing: /home/andriy/amber24/miniconda/bin/pyjson5 -- Installing: /home/andriy/amber24/miniconda/bin/ncursesw6-config -- Installing: /home/andriy/amber24/miniconda/bin/distro -- Installing: /home/andriy/amber24/miniconda/bin/f2py -- Installing: /home/andriy/amber24/miniconda/bin/activate -- Installing: /home/andriy/amber24/miniconda/bin/c_rehash -- Installing: /home/andriy/amber24/miniconda/bin/archspec -- Installing: /home/andriy/amber24/miniconda/bin/sqlite3_analyzer -- Installing: /home/andriy/amber24/miniconda/bin/cython -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-trust -- Installing: /home/andriy/amber24/miniconda/bin/conda-develop -- Installing: /home/andriy/amber24/miniconda/bin/jsonpatch -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-nbconvert -- Installing: /home/andriy/amber24/miniconda/bin/fonttools -- Installing: /home/andriy/amber24/miniconda/bin/propka3 -- Installing: /home/andriy/amber24/miniconda/bin/pcre2-config -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-server -- Installing: /home/andriy/amber24/miniconda/bin/wheel -- Installing: /home/andriy/amber24/miniconda/bin/conda-build -- Installing: /home/andriy/amber24/miniconda/bin/compile_et -- Installing: /home/andriy/amber24/miniconda/bin/dx2cube -- Installing: /home/andriy/amber24/miniconda/bin/curl-config -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-execute -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-labhub -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-troubleshoot -- Installing: /home/andriy/amber24/miniconda/bin/python3.11-config -- Installing: /home/andriy/amber24/miniconda/bin/pkginfo -- Installing: /home/andriy/amber24/miniconda/bin/pdb2pqr30 -- Installing: /home/andriy/amber24/miniconda/bin/pygmentize -- Installing: /home/andriy/amber24/miniconda/bin/jsondiff -- Installing: /home/andriy/amber24/miniconda/bin/pybabel -- Installing: /home/andriy/amber24/miniconda/bin/jsonpointer -- Installing: /home/andriy/amber24/miniconda/bin/xml2-config -- Installing: /home/andriy/amber24/miniconda/bin/zstdless -- Installing: /home/andriy/amber24/miniconda/bin/pip3 -- Installing: /home/andriy/amber24/miniconda/bin/pytest -- Installing: /home/andriy/amber24/miniconda/bin/pip3.11 -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-labextension -- Installing: /home/andriy/amber24/miniconda/bin/bzdiff -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-lab -- Installing: /home/andriy/amber24/miniconda/bin/ttx -- Installing: /home/andriy/amber24/miniconda/bin/bzgrep -- Installing: /home/andriy/amber24/miniconda/bin/krb5-config -- Installing: /home/andriy/amber24/miniconda/bin/zstdgrep -- Installing: /home/andriy/amber24/miniconda/bin/conda -- Installing: /home/andriy/amber24/miniconda/bin/psize -- Installing: /home/andriy/amber24/miniconda/bin/cythonize -- Installing: /home/andriy/amber24/miniconda/bin/cph -- Installing: /home/andriy/amber24/miniconda/bin/conda-convert -- Installing: /home/andriy/amber24/miniconda/bin/conda-render -- Installing: /home/andriy/amber24/miniconda/bin/tqdm -- Installing: /home/andriy/amber24/miniconda/bin/xzless -- Installing: /home/andriy/amber24/miniconda/bin/jsonschema -- Installing: /home/andriy/amber24/miniconda/bin/pip -- Installing: /home/andriy/amber24/miniconda/bin/f90nml -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-kernel -- Installing: /home/andriy/amber24/miniconda/bin/py.test -- Installing: /home/andriy/amber24/miniconda/bin/conda-metapackage -- Installing: /home/andriy/amber24/miniconda/bin/chardetect -- Installing: /home/andriy/amber24/miniconda/bin/k5srvutil -- Installing: /home/andriy/amber24/miniconda/bin/inputgen -- Installing: /home/andriy/amber24/miniconda/bin/bzmore -- Installing: /home/andriy/amber24/miniconda/bin/jupyter-notebook -- Installing: /home/andriy/amber24/miniconda/share/jupyter/kernels/python3/kernel.json -- Installing: /home/andriy/amber24/bin/fftw-wisdom-to-conf -- Installing: /home/andriy/amber24/bin/nc-config -- Installing: /home/andriy/amber24/bin/nf-config -- Installing: /home/andriy/amber24/bin/senergy -- Installing: /home/andriy/amber24/bin/sviol -- Installing: /home/andriy/amber24/bin/sviol2 -- Installing: /home/andriy/amber24/bin/makeCHIR_RST -- Installing: /home/andriy/amber24/bin/makeCSA_RST.na -- Installing: /home/andriy/amber24/bin/makeRIGID_RST -- Installing: /home/andriy/amber24/bin/makeDIP_RST.dna -- Installing: /home/andriy/amber24/bin/makeDIP_RST.protein -- Installing: /home/andriy/amber24/bin/am1bcc -- Installing: /home/andriy/amber24/bin/atomtype -- Installing: /home/andriy/amber24/bin/espgen -- Installing: /home/andriy/amber24/bin/parmcal -- Installing: /home/andriy/amber24/bin/parmchk2 -- Installing: /home/andriy/amber24/bin/prepgen -- Installing: /home/andriy/amber24/bin/residuegen -- Installing: /home/andriy/amber24/bin/respgen -- Installing: /home/andriy/amber24/bin/match -- Installing: /home/andriy/amber24/bin/match_atomname -- Installing: /home/andriy/amber24/bin/antechamber -- Installing: /home/andriy/amber24/bin/bondtype -- Installing: /home/andriy/amber24/bin/reduce -- Installing: /home/andriy/amber24/bin/XrayPrep -- Installing: /home/andriy/amber24/bin/sgldinfo.sh -- Installing: /home/andriy/amber24/bin/sgldwt.sh -- Installing: /home/andriy/amber24/bin/process_mdout.perl -- Installing: /home/andriy/amber24/bin/process_minout.perl -- Installing: /home/andriy/amber24/bin/mdout2pymbar.pl running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib copying build/lib/pyrespgen/constant.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen copying build/lib/pyrespgen/prepin.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen copying build/lib/pyrespgen/zmatrix.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen copying build/lib/pyrespgen/constant_radii.py -> /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen copying build/lib/mdoutanalyzer/windows.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/dataset.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/toplevel_app.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/menus.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/graphproperties.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/mdout.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer copying build/lib/mdoutanalyzer/widgets.py -> /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/constant.py to constant.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/prepin.py to prepin.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/zmatrix.py to zmatrix.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pyrespgen/constant_radii.py to constant_radii.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/windows.py to windows.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/dataset.py to dataset.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/constants.py to constants.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/toplevel_app.py to toplevel_app.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/menus.py to menus.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/graphproperties.py to graphproperties.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/mdout.py to mdout.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/mdoutanalyzer/widgets.py to widgets.cpython-311.pyc running install_egg_info running egg_info writing AmberUtils.egg-info/PKG-INFO writing dependency_links to AmberUtils.egg-info/dependency_links.txt writing top-level names to AmberUtils.egg-info/top_level.txt reading manifest file 'AmberUtils.egg-info/SOURCES.txt' writing manifest file 'AmberUtils.egg-info/SOURCES.txt' removing '/home/andriy/amber24//lib/python3.11/site-packages/AmberUtils-21.0-py3.11.egg-info' (and everything under it) Copying AmberUtils.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/AmberUtils-21.0-py3.11.egg-info running install_scripts copying build/scripts-3.11/fitpkaeo.py -> /home/andriy/amber24//bin copying build/scripts-3.11/mdout_analyzer.py -> /home/andriy/amber24//bin copying build/scripts-3.11/cpeinutil.py -> /home/andriy/amber24//bin copying build/scripts-3.11/genremdinputs.py -> /home/andriy/amber24//bin copying build/scripts-3.11/fixremdcouts.py -> /home/andriy/amber24//bin copying build/scripts-3.11/charmmlipid2amber.py -> /home/andriy/amber24//bin copying build/scripts-3.11/cpinutil.py -> /home/andriy/amber24//bin copying build/scripts-3.11/softcore_setup.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ceinutil.py -> /home/andriy/amber24//bin copying build/scripts-3.11/finddgref.py -> /home/andriy/amber24//bin copying build/scripts-3.11/pyresp_gen.py -> /home/andriy/amber24//bin copying build/scripts-3.11/py_resp.py -> /home/andriy/amber24//bin copying build/scripts-3.11/bar_pbsa.py -> /home/andriy/amber24//bin changing mode of /home/andriy/amber24//bin/fitpkaeo.py to 775 changing mode of /home/andriy/amber24//bin/mdout_analyzer.py to 775 changing mode of /home/andriy/amber24//bin/cpeinutil.py to 775 changing mode of /home/andriy/amber24//bin/genremdinputs.py to 775 changing mode of /home/andriy/amber24//bin/fixremdcouts.py to 775 changing mode of /home/andriy/amber24//bin/charmmlipid2amber.py to 775 changing mode of /home/andriy/amber24//bin/cpinutil.py to 775 changing mode of /home/andriy/amber24//bin/softcore_setup.py to 775 changing mode of /home/andriy/amber24//bin/ceinutil.py to 775 changing mode of /home/andriy/amber24//bin/finddgref.py to 775 changing mode of /home/andriy/amber24//bin/pyresp_gen.py to 775 changing mode of /home/andriy/amber24//bin/py_resp.py to 775 changing mode of /home/andriy/amber24//bin/bar_pbsa.py to 775 -- Installing: /home/andriy/amber24/bin/mm_pbsa.pl -- Installing: /home/andriy/amber24/bin/mm_pbsa_statistics.pl -- Installing: /home/andriy/amber24/bin/FEW.pl -- Installing: /home/andriy/amber24/bin/tleap running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py UPDATING build/lib.linux-x86_64-cpython-311/parmed/_version.py set build/lib.linux-x86_64-cpython-311/parmed/_version.py to '0+unknown' running build_ext building 'parmed.amber._rdparm' extension gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/andriy/amber24_src/AmberTools/src/parmed/src -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-311/src/_rdparm.o gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -I/home/andriy/amber24_src/AmberTools/src/parmed/src -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c src/readparm.cpp -o build/temp.linux-x86_64-cpython-311/src/readparm.o src/readparm.cpp: In function ‘ExitStatus readparm(const std::string&, std::vector >&, ParmDataMap&, ParmStringMap&, ParmStringMap&, ParmFormatMap&, std::string&)’: src/readparm.cpp:143:28: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 8 equals destination size [-Wstringop-truncation] 143 | strncpy(d.c, word.c_str(), MAX_HOLLERITH_SIZE); | ^ g++ -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib build/temp.linux-x86_64-cpython-311/src/_rdparm.o build/temp.linux-x86_64-cpython-311/src/readparm.o -o build/lib.linux-x86_64-cpython-311/parmed/amber/_rdparm.cpython-311-x86_64-linux-gnu.so UPDATING build/lib.linux-x86_64-cpython-311/parmed/_version.py set build/lib.linux-x86_64-cpython-311/parmed/_version.py to '0+unknown' running install_lib copying build/lib.linux-x86_64-cpython-311/parmed/rosetta/pose.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta copying build/lib.linux-x86_64-cpython-311/parmed/rosetta/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta copying build/lib.linux-x86_64-cpython-311/parmed/geometry.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/_version.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/openmm/reporters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm copying build/lib.linux-x86_64-cpython-311/parmed/openmm/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm copying build/lib.linux-x86_64-cpython-311/parmed/openmm/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm copying build/lib.linux-x86_64-cpython-311/parmed/openmm/topsystem.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm copying build/lib.linux-x86_64-cpython-311/parmed/openmm/xmlfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm copying build/lib.linux-x86_64-cpython-311/parmed/openmm/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm copying build/lib.linux-x86_64-cpython-311/parmed/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/rdkit/rdkit.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit copying build/lib.linux-x86_64-cpython-311/parmed/rdkit/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit copying build/lib.linux-x86_64-cpython-311/parmed/utils/netcdf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils copying build/lib.linux-x86_64-cpython-311/parmed/utils/pandautils.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils copying build/lib.linux-x86_64-cpython-311/parmed/utils/decorators.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils copying build/lib.linux-x86_64-cpython-311/parmed/utils/timer.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_lexer.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_input.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/FortranRecordWriter.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_misc.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/FortranRecordReader.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/config.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_output.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_parser.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/_edit_descriptors.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/fortranformat/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat copying build/lib.linux-x86_64-cpython-311/parmed/utils/io.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils copying build/lib.linux-x86_64-cpython-311/parmed/utils/pairlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils copying build/lib.linux-x86_64-cpython-311/parmed/utils/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils copying build/lib.linux-x86_64-cpython-311/parmed/structure.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/scripts.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/tools/checkvalidity.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/addljtype.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/argumentlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/add1264.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/parmlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/sanderapi.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations copying build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations copying build/lib.linux-x86_64-cpython-311/parmed/tools/simulations/openmm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations copying build/lib.linux-x86_64-cpython-311/parmed/tools/parmed_cmd.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/logos.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/actions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/tools/changeradii.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools copying build/lib.linux-x86_64-cpython-311/parmed/symmetry.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/_cpp.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/gromacstop.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/gromacsgro.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/_gromacsfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs copying build/lib.linux-x86_64-cpython-311/parmed/gromacs/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs copying build/lib.linux-x86_64-cpython-311/parmed/topologyobjects.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/formats/pqr.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats copying build/lib.linux-x86_64-cpython-311/parmed/formats/psf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats copying build/lib.linux-x86_64-cpython-311/parmed/formats/mol2.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxContainers.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxReader.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/PdbxWriter.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdbx/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx copying build/lib.linux-x86_64-cpython-311/parmed/formats/pdb.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats copying build/lib.linux-x86_64-cpython-311/parmed/formats/registry.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats copying build/lib.linux-x86_64-cpython-311/parmed/formats/sdf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats copying build/lib.linux-x86_64-cpython-311/parmed/formats/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats copying build/lib.linux-x86_64-cpython-311/parmed/tinker/system.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker copying build/lib.linux-x86_64-cpython-311/parmed/tinker/tinkerfiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker copying build/lib.linux-x86_64-cpython-311/parmed/tinker/topologyobjects.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker copying build/lib.linux-x86_64-cpython-311/parmed/tinker/parameterfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker copying build/lib.linux-x86_64-cpython-311/parmed/tinker/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker copying build/lib.linux-x86_64-cpython-311/parmed/periodic_table.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/residue.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/vec3.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/namd/namdbinfiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd copying build/lib.linux-x86_64-cpython-311/parmed/namd/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd copying build/lib.linux-x86_64-cpython-311/parmed/modeller/data/standard_residues.lib -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data copying build/lib.linux-x86_64-cpython-311/parmed/modeller/data/nonstandard_ccd_residue_templates.json.gz -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data copying build/lib.linux-x86_64-cpython-311/parmed/modeller/data/ccd_residue_templates.json -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/data copying build/lib.linux-x86_64-cpython-311/parmed/modeller/residue.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller copying build/lib.linux-x86_64-cpython-311/parmed/modeller/standardtemplates.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller copying build/lib.linux-x86_64-cpython-311/parmed/modeller/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller copying build/lib.linux-x86_64-cpython-311/parmed/entos/imports.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos copying build/lib.linux-x86_64-cpython-311/parmed/entos/converters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos copying build/lib.linux-x86_64-cpython-311/parmed/entos/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/dlpolyconfig.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly copying build/lib.linux-x86_64-cpython-311/parmed/dlpoly/dlpolyfield.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly copying build/lib.linux-x86_64-cpython-311/parmed/amber/amberformat.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/_chamberparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/netcdffiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/gbnsr6.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/cntrl.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/qmmm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/pb.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/rism.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/mdin.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/ewald.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/typing.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/mdin/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin copying build/lib.linux-x86_64-cpython-311/parmed/amber/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/_tinkerparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/mask.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/titratable_residues.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/readparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/_amberparm.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/offlib.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/_rdparm.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/asciicrd.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_definitions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_math.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/basedimension.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/prefix.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit_operators.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/quantity.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/unit.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/mymatrix.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/standard_dimensions.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/baseunit.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/unit/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit copying build/lib.linux-x86_64-cpython-311/parmed/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed copying build/lib.linux-x86_64-cpython-311/parmed/charmm/psf.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm copying build/lib.linux-x86_64-cpython-311/parmed/charmm/charmmcrds.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm copying build/lib.linux-x86_64-cpython-311/parmed/charmm/parameters.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm copying build/lib.linux-x86_64-cpython-311/parmed/charmm/_charmmfile.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm copying build/lib.linux-x86_64-cpython-311/parmed/charmm/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta/pose.py to pose.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rosetta/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/geometry.py to geometry.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/_version.py to _version.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/reporters.py to reporters.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/utils.py to utils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/parameters.py to parameters.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/topsystem.py to topsystem.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/xmlfile.py to xmlfile.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/openmm/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/constants.py to constants.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit/rdkit.py to rdkit.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/rdkit/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/netcdf.py to netcdf.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/pandautils.py to pandautils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/decorators.py to decorators.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/timer.py to timer.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_lexer.py to _lexer.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_input.py to _input.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/FortranRecordWriter.py to FortranRecordWriter.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_misc.py to _misc.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_exceptions.py to _exceptions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/FortranRecordReader.py to FortranRecordReader.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/config.py to config.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_output.py to _output.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_parser.py to _parser.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/_edit_descriptors.py to _edit_descriptors.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/fortranformat/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/io.py to io.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/pairlist.py to pairlist.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/utils/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/structure.py to structure.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/scripts.py to scripts.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/checkvalidity.py to checkvalidity.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/addljtype.py to addljtype.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/argumentlist.py to argumentlist.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/add1264.py to add1264.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/exceptions.py to exceptions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/parmlist.py to parmlist.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/sanderapi.py to sanderapi.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/simulations/openmm.py to openmm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/parmed_cmd.py to parmed_cmd.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/logos.py to logos.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/actions.py to actions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tools/changeradii.py to changeradii.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/symmetry.py to symmetry.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/exceptions.py to exceptions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/_cpp.py to _cpp.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/gromacstop.py to gromacstop.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/gromacsgro.py to gromacsgro.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/_gromacsfile.py to _gromacsfile.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/gromacs/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/topologyobjects.py to topologyobjects.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/parameters.py to parameters.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pqr.py to pqr.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/psf.py to psf.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/mol2.py to mol2.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxContainers.py to PdbxContainers.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxReader.py to PdbxReader.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/PdbxWriter.py to PdbxWriter.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdbx/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/pdb.py to pdb.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/registry.py to registry.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/sdf.py to sdf.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/system.py to system.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/tinkerfiles.py to tinkerfiles.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/topologyobjects.py to topologyobjects.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/parameterfile.py to parameterfile.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/tinker/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/periodic_table.py to periodic_table.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/residue.py to residue.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/vec3.py to vec3.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd/namdbinfiles.py to namdbinfiles.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/namd/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/residue.py to residue.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/standardtemplates.py to standardtemplates.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/modeller/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/imports.py to imports.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/converters.py to converters.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/entos/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/dlpolyconfig.py to dlpolyconfig.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/dlpoly/dlpolyfield.py to dlpolyfield.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/amberformat.py to amberformat.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_chamberparm.py to _chamberparm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/netcdffiles.py to netcdffiles.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/gbnsr6.py to gbnsr6.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/cntrl.py to cntrl.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/qmmm.py to qmmm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/pb.py to pb.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/rism.py to rism.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/mdin.py to mdin.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/ewald.py to ewald.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/typing.py to typing.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mdin/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/parameters.py to parameters.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_tinkerparm.py to _tinkerparm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/mask.py to mask.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/titratable_residues.py to titratable_residues.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/readparm.py to readparm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/_amberparm.py to _amberparm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/offlib.py to offlib.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/asciicrd.py to asciicrd.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/amber/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_definitions.py to unit_definitions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_math.py to unit_math.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/constants.py to constants.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/basedimension.py to basedimension.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/prefix.py to prefix.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit_operators.py to unit_operators.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/quantity.py to quantity.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/unit.py to unit.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/mymatrix.py to mymatrix.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/standard_dimensions.py to standard_dimensions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/baseunit.py to baseunit.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/unit/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/psf.py to psf.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/charmmcrds.py to charmmcrds.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/parameters.py to parameters.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/_charmmfile.py to _charmmfile.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/parmed/charmm/__init__.py to __init__.cpython-311.pyc running install_egg_info running egg_info writing ParmEd.egg-info/PKG-INFO writing dependency_links to ParmEd.egg-info/dependency_links.txt writing entry points to ParmEd.egg-info/entry_points.txt writing top-level names to ParmEd.egg-info/top_level.txt dependency src/CompatabilityMacros.h won't be automatically included in the manifest: the path doesn't exist reading manifest file 'ParmEd.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'ParmEd.egg-info/SOURCES.txt' removing '/home/andriy/amber24//lib/python3.11/site-packages/ParmEd-0+unknown-py3.11.egg-info' (and everything under it) Copying ParmEd.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/ParmEd-0+unknown-py3.11.egg-info running install_scripts Installing parmed script to /home/andriy/amber24//bin running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts copying and adjusting MMPBSA.py.MPI -> build/scripts-3.11 running install_lib copying build/lib/MMPBSA_mods/timer.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/input_parser.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/output_file.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/API.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/exceptions.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/createinput.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/main.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/infofile.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/findprogs.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/alamdcrd.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/parm_setup.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/commandlineparser.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/fake_mpi.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/calculation.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/make_trajs.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods copying build/lib/MMPBSA_mods/amber_outputs.py -> /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/timer.py to timer.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/input_parser.py to input_parser.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/utils.py to utils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/output_file.py to output_file.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/API.py to API.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/exceptions.py to exceptions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/createinput.py to createinput.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/main.py to main.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/infofile.py to infofile.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/findprogs.py to findprogs.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/alamdcrd.py to alamdcrd.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/parm_setup.py to parm_setup.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/commandlineparser.py to commandlineparser.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/fake_mpi.py to fake_mpi.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/calculation.py to calculation.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/make_trajs.py to make_trajs.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA_mods/amber_outputs.py to amber_outputs.cpython-311.pyc running install_egg_info running egg_info writing MMPBSA.py.egg-info/PKG-INFO writing dependency_links to MMPBSA.py.egg-info/dependency_links.txt writing top-level names to MMPBSA.py.egg-info/top_level.txt reading manifest file 'MMPBSA.py.egg-info/SOURCES.txt' writing manifest file 'MMPBSA.py.egg-info/SOURCES.txt' removing '/home/andriy/amber24//lib/python3.11/site-packages/MMPBSA.py-16.0-py3.11.egg-info' (and everything under it) Copying MMPBSA.py.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/MMPBSA.py-16.0-py3.11.egg-info running install_scripts copying build/scripts-3.11/MMPBSA.py -> /home/andriy/amber24//bin copying build/scripts-3.11/MMPBSA.py.MPI -> /home/andriy/amber24//bin copying build/scripts-3.11/ante-MMPBSA.py -> /home/andriy/amber24//bin changing mode of /home/andriy/amber24//bin/MMPBSA.py to 775 changing mode of /home/andriy/amber24//bin/MMPBSA.py.MPI to 775 changing mode of /home/andriy/amber24//bin/ante-MMPBSA.py to 775 running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib copying build/lib/pymsmt/mol/mol.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/constants.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/pdbio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/mol2io.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/element.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/getlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/cal.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/itfc_dict_table.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/cario.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/gmsio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/amb2chm_typ.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/gauio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/rstio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/sqmio.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/mol/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol copying build/lib/pymsmt/ipmach/calhfe.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach copying build/lib/pymsmt/ipmach/tifiles.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach copying build/lib/pymsmt/ipmach/caliod.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach copying build/lib/pymsmt/ipmach/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach copying build/lib/pymsmt/title.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt copying build/lib/pymsmt/api/AmberParm.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api copying build/lib/pymsmt/api/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api copying build/lib/pymsmt/exp.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt copying build/lib/pymsmt/mcpb/rename_residues.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/mcpb/gene_model_files.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/mcpb/resp_fitting.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/mcpb/amber_modeling.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/mcpb/gene_pre_frcmod_file.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/mcpb/gene_final_frcmod_file.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/mcpb/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/mcpb/fq_model.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb copying build/lib/pymsmt/lib.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt copying build/lib/pymsmt/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pymsmt byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/mol.py to mol.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/constants.py to constants.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/pdbio.py to pdbio.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/mol2io.py to mol2io.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/element.py to element.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/getlist.py to getlist.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/cal.py to cal.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/itfc_dict_table.py to itfc_dict_table.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/cario.py to cario.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/gmsio.py to gmsio.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/amb2chm_typ.py to amb2chm_typ.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/gauio.py to gauio.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/rstio.py to rstio.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/sqmio.py to sqmio.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mol/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/calhfe.py to calhfe.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/tifiles.py to tifiles.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/caliod.py to caliod.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/ipmach/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/title.py to title.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api/AmberParm.py to AmberParm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/api/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/exp.py to exp.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/rename_residues.py to rename_residues.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_model_files.py to gene_model_files.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/resp_fitting.py to resp_fitting.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/amber_modeling.py to amber_modeling.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py to gene_pre_frcmod_file.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py to gene_final_frcmod_file.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/mcpb/fq_model.py to fq_model.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/lib.py to lib.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pymsmt/__init__.py to __init__.cpython-311.pyc running install_egg_info running egg_info writing pyMSMT.egg-info/PKG-INFO writing dependency_links to pyMSMT.egg-info/dependency_links.txt writing top-level names to pyMSMT.egg-info/top_level.txt reading manifest file 'pyMSMT.egg-info/SOURCES.txt' writing manifest file 'pyMSMT.egg-info/SOURCES.txt' removing '/home/andriy/amber24//lib/python3.11/site-packages/pyMSMT-22.0-py3.11.egg-info' (and everything under it) Copying pyMSMT.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/pyMSMT-22.0-py3.11.egg-info running install_scripts copying build/scripts-3.11/metalpdb2mol2.py -> /home/andriy/amber24//bin copying build/scripts-3.11/amb2chm_psf_crd.py -> /home/andriy/amber24//bin copying build/scripts-3.11/espgen.py -> /home/andriy/amber24//bin copying build/scripts-3.11/PdbSearcher.py -> /home/andriy/amber24//bin copying build/scripts-3.11/amb2gro_top_gro.py -> /home/andriy/amber24//bin copying build/scripts-3.11/OptC4.py -> /home/andriy/amber24//bin copying build/scripts-3.11/mol2rtf.py -> /home/andriy/amber24//bin copying build/scripts-3.11/car_to_files.py -> /home/andriy/amber24//bin copying build/scripts-3.11/MCPB.py -> /home/andriy/amber24//bin copying build/scripts-3.11/amb2chm_par.py -> /home/andriy/amber24//bin copying build/scripts-3.11/IPMach.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ProScrs.py -> /home/andriy/amber24//bin copying build/scripts-3.11/CartHess2FC.py -> /home/andriy/amber24//bin changing mode of /home/andriy/amber24//bin/metalpdb2mol2.py to 775 changing mode of /home/andriy/amber24//bin/amb2chm_psf_crd.py to 775 changing mode of /home/andriy/amber24//bin/espgen.py to 775 changing mode of /home/andriy/amber24//bin/PdbSearcher.py to 775 changing mode of /home/andriy/amber24//bin/amb2gro_top_gro.py to 775 changing mode of /home/andriy/amber24//bin/OptC4.py to 775 changing mode of /home/andriy/amber24//bin/mol2rtf.py to 775 changing mode of /home/andriy/amber24//bin/car_to_files.py to 775 changing mode of /home/andriy/amber24//bin/MCPB.py to 775 changing mode of /home/andriy/amber24//bin/amb2chm_par.py to 775 changing mode of /home/andriy/amber24//bin/IPMach.py to 775 changing mode of /home/andriy/amber24//bin/ProScrs.py to 775 changing mode of /home/andriy/amber24//bin/CartHess2FC.py to 775 Copying sander extension source to sanderles... running build running build_py copying sanderles/__init__.py -> /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles running build_ext building 'sanderles.pysander' extension gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -O2 -isystem /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include -fPIC -DLES -I/home/andriy/amber24_src/AmberTools/src/include -I/home/andriy/amber24_src/AmberTools/src/sander -I/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/include/python3.11 -c sanderles/src/pysandermodule.c -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o In file included from sanderles/src/pysandermodule.c:16: /home/andriy/amber24_src/AmberTools/src/sander/sander.h: In function ‘pysander_setup’: /home/andriy/amber24_src/AmberTools/src/sander/sander.h:342:5: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 342 | strncpy(prmtop, prmname, __MAX_FN_LEN); | ^ gcc -pthread -B /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/compiler_compat -shared -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -Wl,-rpath-link,/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib -L/home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-cpython-311/sanderles/src/pysandermodule.o -L/home/andriy/amber24//lib -lsanderles -o /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/pysander.cpython-311-x86_64-linux-gnu.so running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/pysander.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/sanderles copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sanderles/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/sanderles copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sander/pysander.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/sander copying /home/andriy/amber24_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-cpython-311/sander/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/sander byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/sanderles/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/sander/__init__.py to __init__.cpython-311.pyc running install_egg_info running egg_info writing sander.egg-info/PKG-INFO writing dependency_links to sander.egg-info/dependency_links.txt writing top-level names to sander.egg-info/top_level.txt reading manifest file 'sander.egg-info/SOURCES.txt' writing manifest file 'sander.egg-info/SOURCES.txt' removing '/home/andriy/amber24//lib/python3.11/site-packages/sander-22.0-py3.11.egg-info' (and everything under it) Copying sander.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/sander-22.0-py3.11.egg-info running install_scripts /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/dist.py:476: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) sys.argv ['./setup.py', 'build', '-b', '/home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build', '--disable-openmp', 'install', '-f', '--prefix=/home/andriy/amber24/', '--single-version-externally-managed', '--root', '/'] Original compiler envs CXX = /usr/bin/g++ CC = /usr/bin/gcc COMPILER = use_pip = False, cpptraj_home = compile_c_extension = True 2.0.6 use_prebuilt_cythonized_files = False pytraj is inside AMBERHOME using environment: CC=/usr/bin/gcc, CXX=/usr/bin/g++ using CC=/usr/bin/gcc, CXX=/usr/bin/g++ Final compiler envs CXX = /usr/bin/g++ CC = /usr/bin/gcc COMPILER = install = True set rpath to /home/andriy/amber24_src/build/AmberTools/src/cpptraj/src running build running build_py copying pytraj/version.py -> /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj running build_ext running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running install_lib copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/wurlitzer.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/magic.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/externals/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/version.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cython_extra_header/cpp_algorithm.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cython_extra_header copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cython_extra_header/cpp_vector.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cython_extra_header copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/topology_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/nmr.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/vector.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/c_analysis.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/analysis_dict.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/c_analysis.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_analysis/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/energy_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/dihedral_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/dssp_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/base_holder.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/matrix.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/water.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/c_action.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/actionlist.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/c_action.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/actionlist.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/c_action/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/rmsd.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/hbond_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/analysis/nucleic_acid_analysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/decorators.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/Timer.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/convert.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress-circle/progress-circle.js -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress-circle copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress-circle/css/circle.css -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress-circle/css copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/context.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/tools.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/get_common_objects.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/misc.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/cyutils.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/c_commands.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/progress.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/check_and_assert.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/utils/css/oceans16.css -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/css copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/visualization/view.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/visualization/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/topology.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/topology.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/topology/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/coordinfo.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/coordinfo.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/parameter_types.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_core.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_core.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/cpp_vector.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/topology_objects.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_options.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/parameter_types.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_dict.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/topology_objects.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/elements.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/box.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/box.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/c_dict.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/core/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/cast_dataset.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasetlist.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasetlist.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasets.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/c_datasets.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/datasetlist.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/array.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datasets/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/cpp_math.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/cpp_math.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/math/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/testing.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/run_tests.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/testing/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/cluster/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cluster copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/builder/build.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/builder/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/all_actions.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/transform.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/qm.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/TrajectoryBaseIterator.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/lazy.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/sandbox/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/frame.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/trajectory_iterator.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/stripped_trajectory.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/frame.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/frameiter.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/trajectory.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/shared_methods.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/shared_trajectory.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/c_trajout.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/c_trajout.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/c_trajectory.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/c_trajectory.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/trajectory/c_traj/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/io.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/dataset.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/base.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/multiprocess.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/mpi.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/parallel/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/trpcage/trpcage.pdb.gz -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/trpcage copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/trpcage/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/trpcage copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/ala3/Ala3.crd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/ala3/Ala3.top -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/ala3/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/load_samples.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/datafiles.cpython-311-x86_64-linux-gnu.so -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/rna.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/dpdp/DPDP.nc -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/dpdp/DPDP.parm7 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/dpdp/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.000 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/ala2.parm7 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.002 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.003 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/rem.nc.001 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/remd_ala2/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/datafiles.pxd -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/tz2.ortho.parm7 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/tz2.parm7 -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/tz2.ortho.nc -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/tz2.nc -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/tz2/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2 copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/datafiles/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/serialize/serialize.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/serialize/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize copying /home/andriy/amber24_src/build/AmberTools/src/pytraj/CMakeFiles/python-build/lib.linux-x86_64-cpython-311/pytraj/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pytraj byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals/wurlitzer.py to wurlitzer.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals/magic.py to magic.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/externals/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/version.py to version.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/topology_analysis.py to topology_analysis.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/nmr.py to nmr.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/vector.py to vector.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis/analysis_dict.py to analysis_dict.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_analysis/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/energy_analysis.py to energy_analysis.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/dihedral_analysis.py to dihedral_analysis.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/dssp_analysis.py to dssp_analysis.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/base_holder.py to base_holder.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/matrix.py to matrix.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/water.py to water.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/c_action/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/rmsd.py to rmsd.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/hbond_analysis.py to hbond_analysis.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/analysis/nucleic_acid_analysis.py to nucleic_acid_analysis.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/decorators.py to decorators.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/Timer.py to Timer.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/convert.py to convert.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/context.py to context.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/tools.py to tools.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/get_common_objects.py to get_common_objects.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/misc.py to misc.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/c_commands.py to c_commands.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/progress.py to progress.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/utils/check_and_assert.py to check_and_assert.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization/view.py to view.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/visualization/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/topology/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core/elements.py to elements.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/core/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets/datasetlist.py to datasetlist.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets/array.py to array.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datasets/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/math/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing/testing.py to testing.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing/run_tests.py to run_tests.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/testing/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/cluster/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder/build.py to build.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/builder/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/all_actions.py to all_actions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/transform.py to transform.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/qm.py to qm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/TrajectoryBaseIterator.py to TrajectoryBaseIterator.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/lazy.py to lazy.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/sandbox/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/trajectory_iterator.py to trajectory_iterator.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/stripped_trajectory.py to stripped_trajectory.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/frameiter.py to frameiter.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/trajectory.py to trajectory.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/shared_methods.py to shared_methods.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/shared_trajectory.py to shared_trajectory.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/trajectory/c_traj/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/io.py to io.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/dataset.py to dataset.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/base.py to base.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/multiprocess.py to multiprocess.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/mpi.py to mpi.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/parallel/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/trpcage/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/ala3/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/load_samples.py to load_samples.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/dpdp/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/remd_ala2/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/tz2/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/datafiles/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize/serialize.py to serialize.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/serialize/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pytraj/__init__.py to __init__.cpython-311.pyc running install_egg_info running egg_info writing pytraj.egg-info/PKG-INFO writing dependency_links to pytraj.egg-info/dependency_links.txt writing requirements to pytraj.egg-info/requires.txt writing top-level names to pytraj.egg-info/top_level.txt reading manifest file 'pytraj.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'pytraj.egg-info/SOURCES.txt' removing '/home/andriy/amber24//lib/python3.11/site-packages/pytraj-2.0.6-py3.11.egg-info' (and everything under it) Copying pytraj.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/pytraj-2.0.6-py3.11.egg-info running install_scripts running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running install_lib copying build/lib/pdb4amber/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber copying build/lib/pdb4amber/pdb4amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber copying build/lib/pdb4amber/leap_runner.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber copying build/lib/pdb4amber/residue.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber copying build/lib/pdb4amber/template.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber copying build/lib/pdb4amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/utils.py to utils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/pdb4amber.py to pdb4amber.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/leap_runner.py to leap_runner.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/residue.py to residue.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/template.py to template.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber/__init__.py to __init__.cpython-311.pyc running install_egg_info running egg_info writing pdb4amber.egg-info/PKG-INFO writing dependency_links to pdb4amber.egg-info/dependency_links.txt writing entry points to pdb4amber.egg-info/entry_points.txt writing top-level names to pdb4amber.egg-info/top_level.txt reading manifest file 'pdb4amber.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'pdb4amber.egg-info/SOURCES.txt' removing '/home/andriy/amber24//lib/python3.11/site-packages/pdb4amber-22.0-py3.11.egg-info' (and everything under it) Copying pdb4amber.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/pdb4amber-22.0-py3.11.egg-info running install_scripts Installing pdb4amber script to /home/andriy/amber24//bin Inside Amber CMake build system, skipping build of native executables running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying packmol_memgen/lib/utils.py -> build/lib/packmol_memgen/lib running egg_info writing packmol_memgen.egg-info/PKG-INFO writing dependency_links to packmol_memgen.egg-info/dependency_links.txt writing requirements to packmol_memgen.egg-info/requires.txt writing top-level names to packmol_memgen.egg-info/top_level.txt reading manifest file 'packmol_memgen.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'packmol_memgen.egg-info/SOURCES.txt' /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.data' to be distributed and are already explicitly excluding 'packmol_memgen.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.example' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.example' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.example' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.example' to be distributed and are already explicitly excluding 'packmol_memgen.example' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.memembed' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.memembed' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.memembed' to be distributed and are already explicitly excluding 'packmol_memgen.lib.memembed' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.bin' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.memembed.bin' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.memembed.bin' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.memembed.bin' to be distributed and are already explicitly excluding 'packmol_memgen.lib.memembed.bin' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.examples' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.memembed.examples' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.memembed.examples' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.memembed.examples' to be distributed and are already explicitly excluding 'packmol_memgen.lib.memembed.examples' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.scripts' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.memembed.scripts' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.memembed.scripts' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.memembed.scripts' to be distributed and are already explicitly excluding 'packmol_memgen.lib.memembed.scripts' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.memembed.src' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.memembed.src' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.memembed.src' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.memembed.src' to be distributed and are already explicitly excluding 'packmol_memgen.lib.memembed.src' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.packmol' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.packmol' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.packmol' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.packmol' to be distributed and are already explicitly excluding 'packmol_memgen.lib.packmol' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.packmol.docs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.packmol.docs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.packmol.docs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.packmol.docs' to be distributed and are already explicitly excluding 'packmol_memgen.lib.packmol.docs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.packmol.docs.imgs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.packmol.docs.imgs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.packmol.docs.imgs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.packmol.docs.imgs' to be distributed and are already explicitly excluding 'packmol_memgen.lib.packmol.docs.imgs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.pdbremix.data' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.pdbremix.data' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.pdbremix.data' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.pdbremix.data' to be distributed and are already explicitly excluding 'packmol_memgen.lib.pdbremix.data' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/command/build_py.py:207: _Warning: Package 'packmol_memgen.lib.ppm3' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'packmol_memgen.lib.ppm3' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'packmol_memgen.lib.ppm3' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'packmol_memgen.lib.ppm3' to be distributed and are already explicitly excluding 'packmol_memgen.lib.ppm3' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying packmol_memgen/lib/memembed/bin/memembed -> build/lib/packmol_memgen/lib/memembed/bin running build_scripts running install_lib copying build/lib/packmol_memgen/data/memgen.parm -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/leaprc.lipid_ext -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/solvent.parm -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/pdbs.tar.gz -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/lipid_ext.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/frcmod.lipid_ext -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/leaprc.extra_solvents -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/extra_solvents.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/data/frcmod.solvents -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/data copying build/lib/packmol_memgen/example/example.sh -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/example copying build/lib/packmol_memgen/main.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen copying build/lib/packmol_memgen/__version__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen copying build/lib/packmol_memgen/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen copying build/lib/packmol_memgen/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen copying build/lib/packmol_memgen/lib/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib copying build/lib/packmol_memgen/lib/memembed/examples/2x2v.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples copying build/lib/packmol_memgen/lib/memembed/examples/2iahA.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples copying build/lib/packmol_memgen/lib/memembed/examples/2iahA.pot -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples copying build/lib/packmol_memgen/lib/memembed/examples/3o7qA.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/examples copying build/lib/packmol_memgen/lib/memembed/scripts/pymol_membrane_image.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts copying build/lib/packmol_memgen/lib/memembed/scripts/pymol_rotate.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts copying build/lib/packmol_memgen/lib/memembed/bin/memembed -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/bin copying build/lib/packmol_memgen/lib/memembed/bin/.gitignore -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/bin copying build/lib/packmol_memgen/lib/memembed/CMakeLists.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed copying build/lib/packmol_memgen/lib/memembed/LICENSE -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed copying build/lib/packmol_memgen/lib/memembed/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed copying build/lib/packmol_memgen/lib/memembed/src/pdb.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/pdb.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/direct.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/grid.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/main.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/direct.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/ga.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/grid.hpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/src/ga.cpp -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/src copying build/lib/packmol_memgen/lib/memembed/README -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed copying build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber copying build/lib/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber copying build/lib/packmol_memgen/lib/charmmlipid2amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber copying build/lib/packmol_memgen/lib/packmol/title.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/data_types.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/gparc.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/computef.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/gencan.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/restmol.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/comprest.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/comparegrad.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/flashmod.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/fparc.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/setijk.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/release.sh -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/swaptype.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/README.md -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/configure -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/CMakeLists.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/usegencan.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/ahestetic.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/sizes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/LICENSE -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/output.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/writesuccess.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/strlength.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/compute_data.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/heuristics.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/tobar.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/swaptypemod.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/header -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/jacobi.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/cenmass.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/gencan_ieee_signal_routines.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/packmol.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/flashsort.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/resetboxes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/docs/README.md -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img37.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img38.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img36.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img39.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs copying build/lib/packmol_memgen/lib/packmol/docs/imgs/img31.png -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs copying build/lib/packmol_memgen/lib/packmol/docs/imgs/pbc.jpg -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs/imgs copying build/lib/packmol_memgen/lib/packmol/docs/_config.yml -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol/docs copying build/lib/packmol_memgen/lib/packmol/AUTHORS -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/setsizes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/gwalls.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/compile_cmake.sh -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/computeg.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/polartocart.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/input.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/exit_codes.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/getinp.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/setibox.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/pgencan.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/initial.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/random.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/checkpoint.f90 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/packmol/solvate.tcl -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/packmol copying build/lib/packmol_memgen/lib/ppm3/min.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/rmsd.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/watface.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/locate.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/tilting.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/opm.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/orient.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/CMakeLists.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/ppm3_instructions.docx -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/hbcor.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/deftm.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/Makefile -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/res.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/solva.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/license.txt -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/readpdb.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/read_small.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/profile.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/ppm3/find_segm.f -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/ppm3 copying build/lib/packmol_memgen/lib/amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib copying build/lib/packmol_memgen/lib/pdbremix/data/opls.parameter -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/charmm22.parameter -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/phd.frcmod -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/phd.prepin -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/color_b.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/opls.topology -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/binaries.json -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/aminoacid.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/template.pdb -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/znb.leaprc -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/hin.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/znb.frcmod -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/hydroxide.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/charmm22.topology -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/phd.leaprc -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/znb.lib -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/data/make_chi.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data copying build/lib/packmol_memgen/lib/pdbremix/namd.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/pdbatoms.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/spacehash.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/_version.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/data.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/fetch.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/v3.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/force.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/gromacs.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/asa.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/util.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/simulate.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/LICENSE -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/trajectory.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/pymol.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/v3array.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/pdbtext.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/amber.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/rmsd.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/protein.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/v3numpy.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/volume.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix copying build/lib/packmol_memgen/lib/pdbremix/lib/docopt.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib copying build/lib/packmol_memgen/lib/pdbremix/lib/pyqcprot.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib copying build/lib/packmol_memgen/lib/pdbremix/lib/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib copying build/lib/packmol_memgen/lib/tqdm/rich.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/std.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/version.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/dask.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/_tqdm_gui.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/_utils.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/notebook.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/tk.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/asyncio.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/gui.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/auto.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/autonotebook.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/__main__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/_tqdm_pandas.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/_monitor.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/_main.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/_tqdm.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/_tqdm_notebook.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/cli.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/tqdm/tqdm.1 -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm copying build/lib/packmol_memgen/lib/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/main.py to main.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/__version__.py to __version__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/utils.py to utils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts/pymol_membrane_image.py to pymol_membrane_image.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/memembed/scripts/pymol_rotate.py to pymol_rotate.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py to charmmlipid2amber.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/charmmlipid2amber/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/amber.py to amber.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data/color_b.py to color_b.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data/make_chi.py to make_chi.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/namd.py to namd.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbatoms.py to pdbatoms.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/spacehash.py to spacehash.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/_version.py to _version.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/data.py to data.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/fetch.py to fetch.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3.py to v3.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/force.py to force.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/gromacs.py to gromacs.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/asa.py to asa.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/util.py to util.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/simulate.py to simulate.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/trajectory.py to trajectory.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pymol.py to pymol.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3array.py to v3array.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbtext.py to pdbtext.cpython-311.pyc home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/pdbtext.py:30: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/amber.py to amber.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/rmsd.py to rmsd.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/protein.py to protein.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/v3numpy.py to v3numpy.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/volume.py to volume.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/docopt.py to docopt.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/pyqcprot.py to pyqcprot.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/pdbremix/lib/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/rich.py to rich.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/std.py to std.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/version.py to version.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/dask.py to dask.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/utils.py to utils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_gui.py to _tqdm_gui.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_utils.py to _utils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/notebook.py to notebook.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/tk.py to tk.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/asyncio.py to asyncio.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/gui.py to gui.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/auto.py to auto.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/autonotebook.py to autonotebook.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/__main__.py to __main__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_pandas.py to _tqdm_pandas.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_monitor.py to _monitor.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_main.py to _main.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm.py to _tqdm.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/_tqdm_notebook.py to _tqdm_notebook.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/tqdm/cli.py to cli.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen/lib/__init__.py to __init__.cpython-311.pyc running install_egg_info removing '/home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen-2024.3.27-py3.11.egg-info' (and everything under it) Copying packmol_memgen.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/packmol_memgen-2024.3.27-py3.11.egg-info running install_scripts copying build/scripts-3.11/packmol-memgen -> /home/andriy/amber24//bin changing mode of /home/andriy/amber24//bin/packmol-memgen to 775 running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing edgembar.egg-info/PKG-INFO writing dependency_links to edgembar.egg-info/dependency_links.txt writing requirements to edgembar.egg-info/requires.txt writing top-level names to edgembar.egg-info/top_level.txt reading manifest file 'edgembar.egg-info/SOURCES.txt' writing manifest file 'edgembar.egg-info/SOURCES.txt' running build_scripts running install_lib copying build/lib/edgembar/Splines.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/Stage.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/OptUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/Results.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/DiscoverEdges.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/AutoEquil.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/TimeSeriesAnalysis.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/CenteredCubic.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/pkgdata/selerow.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/pkgdata/sorttable.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/pkgdata/edge.css -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/pkgdata/graph.css -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/pkgdata/tschart.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/pkgdata/vis-iface.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/pkgdata/vis-network.min.js -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/pkgdata/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata copying build/lib/edgembar/Trial.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/Edge.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/ImportEdge.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/HtmlUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/Env.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/Graph.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/GraphSearch.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/Names.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/Cli.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar copying build/lib/edgembar/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/edgembar byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Splines.py to Splines.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Stage.py to Stage.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/OptUtils.py to OptUtils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Results.py to Results.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/DiscoverEdges.py to DiscoverEdges.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/AutoEquil.py to AutoEquil.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/TimeSeriesAnalysis.py to TimeSeriesAnalysis.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/CenteredCubic.py to CenteredCubic.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/pkgdata/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Trial.py to Trial.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Edge.py to Edge.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/ImportEdge.py to ImportEdge.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/HtmlUtils.py to HtmlUtils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Env.py to Env.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Graph.py to Graph.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/GraphSearch.py to GraphSearch.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Names.py to Names.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/Cli.py to Cli.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/edgembar/__init__.py to __init__.cpython-311.pyc running install_egg_info removing '/home/andriy/amber24//lib/python3.11/site-packages/edgembar-3.0-py3.11.egg-info' (and everything under it) Copying edgembar.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/edgembar-3.0-py3.11.egg-info running install_scripts copying build/scripts-3.11/edgembar-WriteGraphHtml.py -> /home/andriy/amber24//bin copying build/scripts-3.11/edgembar-amber2dats.py -> /home/andriy/amber24//bin changing mode of /home/andriy/amber24//bin/edgembar-WriteGraphHtml.py to 775 changing mode of /home/andriy/amber24//bin/edgembar-amber2dats.py to 775 running install /home/andriy/amber24_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing ndfes.egg-info/PKG-INFO writing dependency_links to ndfes.egg-info/dependency_links.txt writing requirements to ndfes.egg-info/requires.txt writing top-level names to ndfes.egg-info/top_level.txt reading manifest file 'ndfes.egg-info/SOURCES.txt' writing manifest file 'ndfes.egg-info/SOURCES.txt' running build_scripts running install_lib copying build/lib/ndfes/vFEP.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/gaussian/GaussianOutput.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian copying build/lib/ndfes/gaussian/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian copying build/lib/ndfes/SpatialBin.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/MBAR.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/PCV.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/PathData.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/normalmode/normalmode.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode copying build/lib/ndfes/normalmode/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode copying build/lib/ndfes/normalmode/kie.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode copying build/lib/ndfes/EvalT.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/PlotUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/AutoEquil.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/WAVG.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/GridUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/SpatialDim.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/Trajectory.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/ReadCheckpoint.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/Bspline.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/Metafile.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/VirtualGrid.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/deprecated/OptUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated copying build/lib/ndfes/deprecated/DensityEst.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated copying build/lib/ndfes/deprecated/DensityString.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated copying build/lib/ndfes/deprecated/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated copying build/lib/ndfes/constants/Conversions.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants copying build/lib/ndfes/constants/PeriodicTable.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants copying build/lib/ndfes/constants/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants copying build/lib/ndfes/amber/Restraint.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber copying build/lib/ndfes/amber/Reader.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber copying build/lib/ndfes/amber/Geometry.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber copying build/lib/ndfes/amber/Disang.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber copying build/lib/ndfes/amber/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber copying build/lib/ndfes/SmoothCurve.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/ScriptUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/PathUtils.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/FTSM.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/__init__.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/RBF.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/GPR.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes copying build/lib/ndfes/FES.py -> /home/andriy/amber24//lib/python3.11/site-packages/ndfes byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/vFEP.py to vFEP.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian/GaussianOutput.py to GaussianOutput.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/gaussian/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SpatialBin.py to SpatialBin.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/MBAR.py to MBAR.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PCV.py to PCV.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PathData.py to PathData.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/normalmode.py to normalmode.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/normalmode/kie.py to kie.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/EvalT.py to EvalT.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PlotUtils.py to PlotUtils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/AutoEquil.py to AutoEquil.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/WAVG.py to WAVG.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/GridUtils.py to GridUtils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SpatialDim.py to SpatialDim.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Trajectory.py to Trajectory.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/ReadCheckpoint.py to ReadCheckpoint.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Bspline.py to Bspline.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/Metafile.py to Metafile.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/VirtualGrid.py to VirtualGrid.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/OptUtils.py to OptUtils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/DensityEst.py to DensityEst.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/DensityString.py to DensityString.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/deprecated/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/Conversions.py to Conversions.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/PeriodicTable.py to PeriodicTable.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/constants/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Restraint.py to Restraint.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Reader.py to Reader.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Geometry.py to Geometry.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/Disang.py to Disang.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/amber/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/SmoothCurve.py to SmoothCurve.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/ScriptUtils.py to ScriptUtils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/PathUtils.py to PathUtils.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/FTSM.py to FTSM.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/__init__.py to __init__.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/RBF.py to RBF.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/GPR.py to GPR.cpython-311.pyc byte-compiling /home/andriy/amber24//lib/python3.11/site-packages/ndfes/FES.py to FES.cpython-311.pyc running install_egg_info removing '/home/andriy/amber24//lib/python3.11/site-packages/ndfes-3.0-py3.11.egg-info' (and everything under it) Copying ndfes.egg-info to /home/andriy/amber24//lib/python3.11/site-packages/ndfes-3.0-py3.11.egg-info running install_scripts copying build/scripts-3.11/ndfes-AvgFESs.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ndfes-path-analyzesims.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ndfes-path-prepguess.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ndfes-CombineMetafiles.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ndfes-PrepareAmberData.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ndfes-PrintFES.py -> /home/andriy/amber24//bin copying build/scripts-3.11/ndfes-CheckEquil.py -> /home/andriy/amber24//bin changing mode of /home/andriy/amber24//bin/ndfes-AvgFESs.py to 775 changing mode of /home/andriy/amber24//bin/ndfes-path-analyzesims.py to 775 changing mode of /home/andriy/amber24//bin/ndfes-path-prepguess.py to 775 changing mode of /home/andriy/amber24//bin/ndfes-CombineMetafiles.py to 775 changing mode of /home/andriy/amber24//bin/ndfes-PrepareAmberData.py to 775 changing mode of /home/andriy/amber24//bin/ndfes-PrintFES.py to 775 changing mode of /home/andriy/amber24//bin/ndfes-CheckEquil.py to 775 -- Fixing Miniconda script shebangs CMake Error at /home/andriy/amber24_src/cmake/Replace-function.cmake:32 (file): file failed to open for reading (No such file or directory): /home/andriy/amber24//miniconda/lib/python3.12/site-packages/conda_build/convert.py Call Stack (most recent call first): /home/andriy/amber24_src/cmake/FixCondaShebang/FixCondaShebang.cmake:48 (configuretime_file_replace)