ERROR: Error [Errno 2] No such file or directory: 'git' while executing command git version

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Nandha Kumar

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Jun 25, 2023, 10:45:29 AM6/25/23
to gmx_MMPBSA
Good evening Mam/Sir

I ran the following command .And subsequent error occurred . Please help to fix it.


(gmxMMPBSA) mohammed@Naveez:~$ 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-uycnypjo
  ERROR: Error [Errno 2] No such file or directory: 'git' while executing command git version
ERROR: Cannot find command 'git' - do you have 'git' installed and in your PATH?
Screenshot from 2023-06-25 20-10-29.png

Mario Sergio Valdes

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Jun 25, 2023, 7:29:32 PM6/25/23
to gmx_MMPBSA
Please, install git either from the system repository (sudo apt install git) or using conda (conda install -c anaconda git)

Nandha Kumar

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Jun 26, 2023, 12:09:04 AM6/26/23
to gmx_MMPBSA
Yes, Mam or Sir, this problem is solved, but again the same command comes up with another error.

Command line- python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

Error
(gmxMMPBSA) mohammed@Naveez:~$ 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-cgx7thbe
  Running command git clone --filter=blob:none --quiet https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-cgx7thbe
  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
  ╰─> [160 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/periodic_table.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/topologyobjects.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/_version.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/vec3.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/scripts.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/constants.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/parameters.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/structure.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/symmetry.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/residue.py -> build/lib.linux-x86_64-cpython-39/parmed
      copying parmed/geometry.py -> build/lib.linux-x86_64-cpython-39/parmed
      creating 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/parameters.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/mask.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/__init__.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/_tinkerparm.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/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/parameterfile.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/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
      copying parmed/tinker/__init__.py -> build/lib.linux-x86_64-cpython-39/parmed/tinker
      creating 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/constants.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/mymatrix.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/unit_definitions.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/unit_operators.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/__init__.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/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/gbnsr6.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
      copying parmed/amber/mdin/__init__.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/qmmm.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/mdin.py -> build/lib.linux-x86_64-cpython-39/parmed/amber/mdin
      creating 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/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/_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/PdbxWriter.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/PdbxReader.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/pose.py -> build/lib.linux-x86_64-cpython-39/parmed/rosetta
      copying parmed/rosetta/__init__.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/pqr.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/__init__.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/pdb.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/FortranRecordReader.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/config.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/_output.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/_misc.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/_parser.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
      creating 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/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/utils.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/utils/timer.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/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/netcdf.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/six.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      copying parmed/utils/decorators.py -> build/lib.linux-x86_64-cpython-39/parmed/utils
      creating 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/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/_cpp.py -> build/lib.linux-x86_64-cpython-39/parmed/gromacs
      creating 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/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/exceptions.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/addljtype.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/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
      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/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/__init__.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
      copying parmed/tools/gui/_guiactions.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/__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
      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/mohammed//envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/mohammed//envs/gmxMMPBSA/include -fPIC -O2 -isystem /home/mohammed//envs/gmxMMPBSA/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/mohammed//envs/gmxMMPBSA/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/mohammed//envs/gmxMMPBSA/include -fPIC -I/tmp/pip-req-build-cgx7thbe/src -I/home/mohammed/\/envs/gmxMMPBSA/include/python3.9 -c src/_rdparm.cpp -o build/temp.linux-x86_64-cpython-39/src/_rdparm.o
      error: command '/home/mohammed//envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc' failed: No such file or directory
      [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



And I checked for this error in previews mail and said that downgrade the compilers package. Install compilers=1.2.0. using conda install -c conda-forge compilers=1.2.0 this command, but after this command as well, it comes with the same error.

Mario Sergio Valdes

unread,
Jun 26, 2023, 10:35:33 AM6/26/23
to gmx_MMPBSA
To save time, we recommend installing gmx_MMPBSA using the env.yml file, which contains all the correct dependencies. In this way, you avoid library incompatibility. (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/#installing-gmx_mmpbsa-v15x)
Let me know if this works for you

Nandha Kumar

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Jun 26, 2023, 2:00:14 PM6/26/23
to gmx_MMPBSA
Yes mam  i try with env.yml file 
Commands
1. conda env create -n gmxMMPBSA --file env.yml
2. conda activate gmxMMPBSA
after this two command, ill try the previws commands that is 1. conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers=1.2.0 -y -q
2.  python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4After this command i getting same error error: command '/home/mohammed//envs/gmxMMPBSA/bin/x86_64-conda-linux-gnu-cc' failed: No such file or directory

      [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
Screenshot from 2023-06-26 23-29-10.png

Mario Sergio Valdes

unread,
Jun 26, 2023, 3:59:16 PM6/26/23
to gmx_MMPBSA
Using the env.yml installation method it create a ready-to-run conda environment. So, you don't need to reinstall anything
Commands
1. conda env create -n gmxMMPBSA --file env.yml
2. conda activate gmxMMPBSAFrom here, you can use gmx_MMPBSA with no problem

Nandha Kumar

unread,
Jun 26, 2023, 11:37:27 PM6/26/23
to gmx_MMPBSA
After enter those command to run the gmxMMPBSA 

command 
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_10.tpr -ci index.ndx -cg 1 13 -ct md_0_1_noPBC.xtc -cp topol.top

one error is coming 

gmx_MMPBSA: command not found
Screenshot from 2023-06-27 09-07-05.png

Mario Sergio Valdes

unread,
Jun 27, 2023, 2:54:48 AM6/27/23
to gmx_MMPBSA
I can't reproduce this problem. In the image, conda is terminating in error, so it looks like there is a problem. On my PC, it works without problems. Please make sure you have the latest version of conda installed and that there are no errors before running gmx_MMPBSA
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