Error solving.

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Harshada Sawant

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Jul 10, 2023, 3:41:12 AM7/10/23
to gmx_MMPBSA
Good afternoon,
I am Ms Harshada , a beginner in learning Molecular Dynamics Simulation studies. So i ran the code for gmx MMPBSaA during which I faced this error where it was showing that " gmx_MMPBSA does not support water/ions molecules in any structure, but we found 835 molecules in the complex." 
So kindly guide me further details with it.
gmx_MMPBSA.log

marioe911116

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Jul 10, 2023, 5:31:40 AM7/10/23
to gmx_MMPBSA
update Parmed as follows:


and see if that solves the issue

Harshada Sawant

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Jul 10, 2023, 6:08:02 AM7/10/23
to marioe911116, gmx_MMPBSA
I run the above given code its showing this error

(gmxMMPBSA) chemo@DESKTOP-KF1QR91:~$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
  Cloning https://github.com/Valdes-Tresanco-MS/ParmEd.git (to revision v3.4) to /tmp/pip-req-build-3m1knizt
  Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-3m1knizt
  Running command git checkout -b v3.4 --track origin/v3.4
  Switched to a new branch 'v3.4'
  Branch 'v3.4' set up to track remote branch 'v3.4' from 'origin'.
  Resolved https://github.com/Valdes-Tresanco-MS/ParmEd.git to commit 41cc9ab1fe930f0c13c36433148d4601307d60c3
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: ParmEd
  Building wheel for ParmEd (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [167 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-39
      creating build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/geometry.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/structure.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/vec3.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/scripts.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed
      creating build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/_tinkerparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/mask.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/netcdffiles.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/titratable_residues.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/readparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/_amberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/amberformat.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/asciicrd.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      creating build/lib.linux-x86_64-cpython-39/parmed/modeller
      copying parmed/modeller/residue.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
      copying parmed/modeller/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
      copying parmed/modeller/standardtemplates.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
      creating build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/parameterfile.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/tinkerfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      creating build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit_math.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/mymatrix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/constants.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit_operators.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/prefix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/standard_dimensions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/quantity.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/baseunit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit_definitions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/basedimension.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      creating build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/cntrl.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/mdin.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/qmmm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/pb.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/ewald.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/gbnsr6.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      creating build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/charmmcrds.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      creating build/lib.linux-x86_64-cpython-39/parmed/formats
      creating build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/PdbxReader.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/PdbxContainers.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/PdbxWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      creating build/lib.linux-x86_64-cpython-39/parmed/rosetta
      copying parmed/rosetta/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
      copying parmed/rosetta/pose.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
      creating build/lib.linux-x86_64-cpython-39/parmed/rdkit
      copying parmed/rdkit/rdkit.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
      copying parmed/rdkit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
      copying parmed/formats/pdb.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/registry.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/sdf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      creating build/lib.linux-x86_64-cpython-39/parmed/utils
      creating build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/FortranRecordReader.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_misc.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/FortranRecordWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_parser.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_input.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_lexer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/config.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_edit_descriptors.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_output.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      creating build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/topsystem.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/xmlfile.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/utils.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/utils/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/io.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/netcdf.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/pairlist.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/decorators.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/six.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      creating build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/gromacsgro.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/_cpp.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      creating build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/checkvalidity.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/parmlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/add1264.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/logos.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/actions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/argumentlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/parmed_cmd.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/changeradii.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/coarsegrain.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      creating build/lib.linux-x86_64-cpython-39/parmed/namd
      copying parmed/namd/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
      copying parmed/namd/namdbinfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
      creating build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/_guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/guitools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/guifiletools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/_guiwidgets.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      creating build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      copying parmed/tools/simulations/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      copying parmed/tools/simulations/sanderapi.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      copying parmed/tools/simulations/openmm.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      creating build/lib.linux-x86_64-cpython-39/parmed/modeller/data
      copying parmed/modeller/data/standard_residues.lib -> build/lib.linux-x86_64-cpython-39/parmed/modeller/data
      UPDATING build/lib.linux-x86_64-cpython-39/parmed/_version.py
      set build/lib.linux-x86_64-cpython-39/parmed/_version.py to '3.4.3+11.g41cc9ab'
      running build_ext
      building 'parmed.amber._rdparm' extension
      creating build/temp.linux-x86_64-cpython-39
      creating build/temp.linux-x86_64-cpython-39/src
      /home/chemo/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-3m1knizt/src -I/home/chemo/miniconda3/envs/gmxMMPBSA/include/python3.9 -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-39/src/_rdparm.o
      In file included from /home/chemo/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
                       from /home/chemo/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/locale:41,
                       from src/readparm.h:5,
                       from src/_rdparm.cpp:17:
      /home/chemo/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::'
         80 |   using ::timespec_get;
            |           ^~~~~~~~~~~~
      error: command '/home/chemo/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for ParmEd
  Running setup.py clean for ParmEd
Failed to build ParmEd
Installing collected packages: ParmEd
  Attempting uninstall: ParmEd
    Found existing installation: ParmEd 3.4.3
    Uninstalling ParmEd-3.4.3:
      Successfully uninstalled ParmEd-3.4.3
  Running setup.py install for ParmEd ... error
  error: subprocess-exited-with-error

  × Running setup.py install for ParmEd did not run successfully.
  │ exit code: 1
  ╰─> [180 lines of output]
      running install
      /home/chemo/miniconda3/envs/gmxMMPBSA/lib/python3.9/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, pypa/build or
              other standards-based tools.

              ********************************************************************************

      !!
        self.initialize_options()
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-cpython-39
      creating build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/geometry.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/structure.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/vec3.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/scripts.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed
      creating build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/offlib.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/_tinkerparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/mask.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/netcdffiles.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/titratable_residues.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/readparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/_amberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/amberformat.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/asciicrd.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      creating build/lib.linux-x86_64-cpython-39/parmed/modeller
      copying parmed/modeller/residue.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
      copying parmed/modeller/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
      copying parmed/modeller/standardtemplates.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
      creating build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/parameterfile.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      copying parmed/tinker/tinkerfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      creating build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit_math.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/mymatrix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/constants.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit_operators.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/prefix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/standard_dimensions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/quantity.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/baseunit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/unit_definitions.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/basedimension.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      creating build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/cntrl.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/mdin.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/qmmm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/pb.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/rism.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/ewald.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      copying parmed/amber/mdin/gbnsr6.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      creating build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/charmmcrds.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/_charmmfile.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      copying parmed/charmm/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/charmm
      creating build/lib.linux-x86_64-cpython-39/parmed/formats
      creating build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/PdbxReader.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/PdbxContainers.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      copying parmed/formats/pdbx/PdbxWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/formats/pdbx
      creating build/lib.linux-x86_64-cpython-39/parmed/rosetta
      copying parmed/rosetta/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
      copying parmed/rosetta/pose.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
      creating build/lib.linux-x86_64-cpython-39/parmed/rdkit
      copying parmed/rdkit/rdkit.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
      copying parmed/rdkit/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/rdkit
      copying parmed/formats/pdb.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/pqr.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/registry.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/mol2.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/sdf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      copying parmed/formats/psf.py -> build/lib.linux-x86_64-cpython-39/parmed/formats
      creating build/lib.linux-x86_64-cpython-39/parmed/utils
      creating build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/FortranRecordReader.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_misc.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/FortranRecordWriter.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_parser.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_input.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_lexer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/config.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_edit_descriptors.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      copying parmed/utils/fortranformat/_output.py -> build/lib.linux-x86_64-cpython-39/parmed/utils/fortranformat
      creating build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/topsystem.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/xmlfile.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/openmm/utils.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/utils/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/io.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/netcdf.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/pairlist.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/decorators.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/timer.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/six.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      creating build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/_gromacsfile.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/gromacsgro.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/_cpp.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      creating build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/checkvalidity.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/parmlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/add1264.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/logos.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/actions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/argumentlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/parmed_cmd.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/changeradii.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/coarsegrain.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/exceptions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      creating build/lib.linux-x86_64-cpython-39/parmed/namd
      copying parmed/namd/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
      copying parmed/namd/namdbinfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
      creating build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/_guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/guitools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/guiactions.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/guifiletools.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      copying parmed/tools/gui/_guiwidgets.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/gui
      creating build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      copying parmed/tools/simulations/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      copying parmed/tools/simulations/sanderapi.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      copying parmed/tools/simulations/openmm.py -> build/lib.linux-x86_64-cpython-39/parmed/tools/simulations
      creating build/lib.linux-x86_64-cpython-39/parmed/modeller/data
      copying parmed/modeller/data/standard_residues.lib -> build/lib.linux-x86_64-cpython-39/parmed/modeller/data
      UPDATING build/lib.linux-x86_64-cpython-39/parmed/_version.py
      set build/lib.linux-x86_64-cpython-39/parmed/_version.py to '3.4.3+11.g41cc9ab'
      running build_ext
      building 'parmed.amber._rdparm' extension
      creating build/temp.linux-x86_64-cpython-39
      creating build/temp.linux-x86_64-cpython-39/src
      /home/chemo/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/chemo/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-3m1knizt/src -I/home/chemo/miniconda3/envs/gmxMMPBSA/include/python3.9 -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-39/src/_rdparm.o
      In file included from /home/chemo/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
                       from /home/chemo/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/locale:41,
                       from src/readparm.h:5,
                       from src/_rdparm.cpp:17:
      /home/chemo/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/ctime:80:11: error: 'timespec_get' has not been declared in '::'
         80 |   using ::timespec_get;
            |           ^~~~~~~~~~~~
      error: command '/home/chemo/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  Rolling back uninstall of ParmEd
  Moving to /home/chemo/miniconda3/envs/gmxMMPBSA/bin/parmed
   from /tmp/pip-uninstall-2e5bew14/parmed
  Moving to /home/chemo/miniconda3/envs/gmxMMPBSA/bin/xparmed
   from /tmp/pip-uninstall-2e5bew14/xparmed
  Moving to /home/chemo/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/ParmEd-3.4.3.dist-info/
   from /home/chemo/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/~armEd-3.4.3.dist-info
  Moving to /home/chemo/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/
   from /home/chemo/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/~armed
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> ParmEd

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
Thanks and Regards 
Harshada Sawant


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Mario Sergio Valdes

unread,
Jul 10, 2023, 12:13:51 PM7/10/23
to gmx_MMPBSA
Please, downgrade compilers package version (conda install compilers=1.2.0) and then try to install parmed
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