ERROR: Could not build wheels for ParmEd, which is required to install pyproject.toml-based projects

[Sarthak Trivedi SVNIT]

                                                                 -------ERROR-------

(gmxMMPBSA) xyz@xyz-System-Product-Name:~$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Collecting 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-4u9wy6gh
  Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-4u9wy6gh
  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/vec3.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/geometry.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/structure.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
      copying parmed/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/symmetry.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
      creating 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/titratable_residues.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/asciicrd.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/amberformat.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/readparm.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/mask.py -> 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/_chamberparm.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      copying parmed/amber/netcdffiles.py -> build/lib.linux-x86_64-cpython-39/parmed/amber
      creating build/lib.linux-x86_64-cpython-39/parmed/modeller
      copying parmed/modeller/standardtemplates.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/residue.py -> build/lib.linux-x86_64-cpython-39/parmed/modeller
      creating 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/topologyobjects.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
      copying parmed/tinker/system.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      creating 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/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/unit_definitions.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/unit.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/prefix.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/basedimension.py -> 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/unit_operators.py -> build/lib.linux-x86_64-cpython-39/parmed/unit
      copying parmed/unit/baseunit.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/qmmm.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
      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/__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/ewald.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
      creating 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/parameters.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/__init__.py -> 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/PdbxWriter.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
      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/__init__.py -> 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/formats/pdb.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/mol2.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/pqr.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/_input.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
      copying parmed/utils/fortranformat/_edit_descriptors.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/_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/config.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/_parser.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
      creating 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/__init__.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/parameters.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/openmm/reporters.py -> build/lib.linux-x86_64-cpython-39/parmed/openmm
      copying parmed/utils/io.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/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
      copying parmed/utils/pairlist.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/decorators.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/pandautils.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      creating build/lib.linux-x86_64-cpython-39/parmed/gromacs
      copying parmed/gromacs/_cpp.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/__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/gromacstop.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      creating 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/add1264.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/exceptions.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/checkvalidity.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/argumentlist.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/logos.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/addljtype.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      copying parmed/tools/parmlist.py -> build/lib.linux-x86_64-cpython-39/parmed/tools
      creating build/lib.linux-x86_64-cpython-39/parmed/namd
      copying parmed/namd/namdbinfiles.py -> build/lib.linux-x86_64-cpython-39/parmed/namd
      copying parmed/namd/__init__.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/guitools.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/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/_guiactions.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/openmm.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/__init__.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/drr-18/miniconda3/envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/drr-18/miniconda3/envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-4u9wy6gh/src -I/home/drr-18/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/drr-18/miniconda3/envs/gmxMMPBSA/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/locale_facets_nonio.h:39,
                       from /home/drr-18/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/drr-18/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/drr-18/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
ERROR: Could not build wheels for ParmEd, which is required to install pyproject.toml-based projects

PLEASE HELP ME TO SOLVE THIS ERROR FOR THE INSTALLATION OF GMX_MMPBSA (I AM TRYING TO INSTALL AN OLDER VERSION TO ANALYSE MY OLD CALCULATED FILES).

[Mario Sergio Valdes]

If you are installing an old version, make sure that you install compilers=1.2

[Sarthak Trivedi SVNIT]

(gmxMMPBSA) xyz@xyz-System-Product-Name:~$ conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers=1.2 -y -q
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/main/linux-64/repodata.json>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

If your current network has https://www.anaconda.com blocked, please file
a support request with your network engineering team.

'https//repo.anaconda.com/pkgs/main/linux-64'

THIS IS THE ERROR, AFTER ADDING "compilers=1.2" TO THE COMMAND LINE. I ALSO TRIED TO INSTALL BY env.yml FILE, BUT I CAN'T INSTALL IT SUCCESSFULLY. 

[Mario Sergio Valdes]

It seems to be more of an internet connection problem than an installation problem. Are you using a VPN or do you have administrative restrictions?

[Sarthak Trivedi SVNIT]

Thank you sir, when i installed into a very high speed network. It got installed successfully. But it is suggesting to rewrite output by using command "gmx_MMPBSA --rewrite-output". Once i run it it gives me the error as following:


(gmxMMPBSA) xyz@xyz-System-Product-Name:~/Complex_02_50ns_MMPBSA$ gmx_MMPBSA --rewrite-output
[INFO   ] Starting gmx_MMPBSA v1.6.1
[INFO   ] Command-line
  gmx_MMPBSA --rewrite-output

tets
[INFO   ] Loading and checking parameter files for compatibility...
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 106, in gmxmmpbsa
    app.loadcheck_prmtops()
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 731, in loadcheck_prmtops
    self.normal_system.CheckConsistency()
  File "/home/drr-18/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/parm_setup.py", line 839, in CheckConsistency
    raise PrmtopError('Topology files have inconsistent RADIUS_SETs')
PrmtopError: Topology files have inconsistent RADIUS_SETs
Exiting. All files have been retained.



CAN YOU COMMENT ON THIS ERROR TO SAVE MY FILE? I AM IN HURRY TO REGENERATE GRAPHS AND DATA BY GMX_MMPBSA_ANA ON URGENT BASIS. IT WOULD BE A GREAT HELP TO SAVE MY TIME. THANK YOU IN ADVANCE.

[Mario Sergio Valdes]

Please, zip your work folder, excluding the path files, and send it to my email to help you.

[Sarthak Trivedi SVNIT]

Hello Sir,

Thank you so much for your response. I am happy to inform you that i could solve it by observing the prmtop files of complex, ligand and receptor. It was found that Radius set didn't match. During data transfer i mistakenly transferred other calculation data file into a wrong folder.