gmx_MMPBSA installation error please help

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imren bayıl

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Nov 18, 2022, 6:27:27 PM11/18/22
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I am trying to install gmx_MMPBSA ubuntu app on windows.
I used these commands respectively.
sudo apt install openmpi-bin libopenmpi-dev openssh-client
 sudo apt-get install python
 sudo apt-get install python3-pip 
sudo apt-get upgrade 
sudo apt-get update
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 
chmod +x Miniconda3-latest-Linux-x86_64.sh 
./Miniconda3-latest-Linux-x86_64.sh 
conda update conda 
conda create -n gmxMMPBSA python=3.9 -y -q 
conda activate gmxMMPBSA 
conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q 
python -m pip install git+https://github.com/Valdes-Tresanco-MS... 
python -m pip install pyqt5 
python -m pip install gmx_MMPBSA 
evertyhing goes well but after gmx_MMPBSA_test it gives error
[INFO   ] Cloning gmx_MMPBSA repository in /mnt/g/Amber/amber20/gmx_MMPBSA_test
Cloning into '/mnt/g/Amber/amber20/gmx_MMPBSA_test'...
remote: Enumerating objects: 19519, done.
remote: Counting objects: 100% (201/201), done.
remote: Compressing objects: 100% (75/75), done.
remote: Total 19519 (delta 77), reused 179 (delta 68), pack-reused 19318
Receiving objects: 100% (19519/19519), 325.44 MiB | 1.52 MiB/s, done.
Resolving deltas: 100% (13750/13750), done.
Checking out files: 100% (678/678), done.
[INFO   ] Cloning gmx_MMPBSA repository...Done.
[INFO   ]                           Example                                STATE
--------------------------------------------------------------------------------
[INFO   ] Protein-Ligand (Single trajectory approximation)               RUNNING
[ERROR  ] Protein-Ligand (Single trajectory approximation)       [ 1/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_ligand/ST/3.log)
[INFO   ] Protein-Protein                                                RUNNING
[ERROR  ] Protein-Protein                                        [ 2/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_protein/4.log)
[INFO   ] Protein-DNA                                                    RUNNING
[ERROR  ] Protein-DNA                                            [ 3/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_DNA/5.log)
[INFO   ] Protein-Glycan                                                 RUNNING
[ERROR  ] Protein-Glycan                                         [ 4/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_glycan/7.log)
[INFO   ] Comp_receptor                                                  RUNNING
[ERROR  ] Comp_receptor                                          [ 5/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Comp_receptor/9.log)
[INFO   ] Alanine Scanning                                               RUNNING
[ERROR  ] Alanine Scanning                                       [ 6/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Alanine_scanning/12.log)
[INFO   ] Stability calculation                                          RUNNING
[ERROR  ] Stability calculation                                  [ 7/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Stability/13.log)
[INFO   ] Decomposition Analysis                                         RUNNING
[ERROR  ] Decomposition Analysis                                 [ 8/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Decomposition_analysis/14.log)
[INFO   ] Interaction Entropy approximation                              RUNNING
[ERROR  ] Interaction Entropy approximation                      [ 9/ 9]   ERROR
           Please, check the test log
           (/mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Entropy_calculations/Interaction_Entropy/15.log)
Could anybody help me how to fix error?
I struggle to solve this issue for two days.


Mario Sergio Valdes

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Nov 18, 2022, 6:53:45 PM11/18/22
to gmx_MMPBSA
Do you have Gromacs installed? Please check the log file of each calculation to know what is the error (e.g., less /mnt/g/Amber/amber20/gmx_MMPBSA_test/examples/Protein_protein/4.log).

imren bayıl

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Nov 18, 2022, 7:39:46 PM11/18/22
to gmx_MMPBSA
G:\Amber\amber20\gmx_MMPBSA_test\examples\Protein_protein
I checked it 
Traceback (most recent call last):
  File "/home/haruki/.local/bin/gmx_MMPBSA", line 7, in <module>
    from GMXMMPBSA.app import gmxmmpbsa
  File "/home/haruki/.local/lib/python2.7/site-packages/GMXMMPBSA/app.py", line 145
    sys.exit(app.exec())
                    ^
SyntaxError: invalid syntax
Traceback (most recent call last):
  File "/home/haruki/.local/bin/gmx_MMPBSA", line 7, in <module>
    from GMXMMPBSA.app import gmxmmpbsa
  File "/home/haruki/.local/lib/python2.7/site-packages/GMXMMPBSA/app.py", line 145
    sys.exit(app.exec())
                    ^
SyntaxError: invalid syntax
Traceback (most recent call last):
  File "/home/haruki/.local/bin/gmx_MMPBSA", line 7, in <module>
    from GMXMMPBSA.app import gmxmmpbsa
  File "/home/haruki/.local/lib/python2.7/site-packages/GMXMMPBSA/app.py", line 145
    sys.exit(app.exec())
                    ^
SyntaxError: invalid syntax
Traceback (most recent call last):
  File "/home/haruki/.local/bin/gmx_MMPBSA", line 7, in <module>
    from GMXMMPBSA.app import gmxmmpbsa
  File "/home/haruki/.local/lib/python2.7/site-packages/GMXMMPBSA/app.py", line 145
    sys.exit(app.exec())
                    ^
SyntaxError: invalid syntax
so What is the error ? 
19 Kasım 2022 Cumartesi tarihinde saat 01:53:45 UTC+2 itibarıyla mariosergi...@gmail.com şunları yazdı:

Mario Sergio Valdes

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Nov 18, 2022, 9:02:45 PM11/18/22
to gmx_MMPBSA
gmx_MMPBSA is incompatible with Python 2. Please, follow the installation instructions (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/)

imren bayıl

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Nov 19, 2022, 5:14:59 AM11/19/22
to gmx_MMPBSA
hi,I uptaded python version 2 to python 3.8 
but after writing ;gmx_MMPBSA_test

Traceback (most recent call last):
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/bin/gmx_MMPBSA_test", line 8, in <module>
    sys.exit(gmxmmpbsa_test())
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 159, in gmxmmpbsa_test
    run_test(parser)
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/tester.py", line 85, in run_test
    shutil.rmtree(gmx_mmpbsa_test_folder)
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/lib/python3.8/shutil.py", line 718, in rmtree
    _rmtree_safe_fd(fd, path, onerror)
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
    _rmtree_safe_fd(dirfd, fullname, onerror)
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/lib/python3.8/shutil.py", line 655, in _rmtree_safe_fd
    _rmtree_safe_fd(dirfd, fullname, onerror)
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/lib/python3.8/shutil.py", line 659, in _rmtree_safe_fd
    onerror(os.rmdir, fullname, sys.exc_info())
  File "/mnt/g/Amber/amber20/ls/envs/gmxMMPBSA/lib/python3.8/shutil.py", line 657, in _rmtree_safe_fd
    os.rmdir(entry.name, dir_fd=topfd)
PermissionError: [Errno 13] Permission denied: 'ST'
Do you have a solution ?
19 Kasım 2022 Cumartesi tarihinde saat 04:02:45 UTC+2 itibarıyla mariosergi...@gmail.com şunları yazdı:

Mario Sergio Valdes

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Nov 19, 2022, 11:58:47 AM11/19/22
to gmx_MMPBSA
This error is probably because you do not have "write" permission on the folder you are working on. /mnt/... folder/subfolder usually only allows you to mount files, disks, or devices. However, in most cases, this folder does not allow modifications. Since you are working on a local machine, ideally you should use your home to do any process that requires file generation and/or modification.

imren bayıl

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Nov 19, 2022, 6:46:27 PM11/19/22
to gmx_MMPBSA
Hİ,I have installed MMPBSA my  computer which is just consist of ubuntu.I used this commands respectively.I didint get any error.
gmx_MMPBSA_test -v
gmx_MMPBSA_test v1.5.7 based on MMPBSA version 16.0 is writing
I am getting error.I attached my screenshot.MMPBSA has been installed.but I am getting error.Could you guide me please ,I have to use this tool for my phd thesis.
Thanks
  1. Download miniconda
  2. bash Miniconda3-latest-Linux-x86_64.sh
  3. Make sure conda is already in the path with: nano ~/.bashrc
  4. Restart terminal
  5. sudo apt install git
  1. conda update conda
  2. conda create -n gmxMMPBSA python=3.9 -y -q
  3. conda activate gmxMMPBSA
  4. conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q
  1. python -m pip install pyqt5
  2. python -m pip install gmx_MMPBSA
  1. python -m pip install gmx_MMPBSA -U
for tutorial
gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc
[INFO   ] Starting gmx_MMPBSA v1.5.7
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 1 13 -ct com_traj.xtc

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /usr/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Generating AMBER Compatible PDB Files...
[INFO   ] Changing the Complex residues name format from GROMACS to AMBER...
[INFO   ] Changing the Receptor residues name format from GROMACS to AMBER...
[INFO   ] Changing the Ligand residues name format from GROMACS to AMBER...
[INFO   ] Splitting  receptor and ligand in PDB files..
[INFO   ] Building tleap input files...
[ERROR  ] MMPBSA_Error /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 548, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 121, in buildTopology
    tops = self.makeToptleap()
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1383, in makeToptleap
    self._run_tleap(tleap, 'leap.in', data_path)
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 1510, in _run_tleap
    GMXMMPBSA_ERROR('%s failed when querying %s' % (tleap, self.FILES.prefix + arg1))
  File "/home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
    raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /home/imren/Downloads/home/imren/Downloads/miniconda33/envs/gmxMMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
1.png2.png4.png5.png7.png
19 Kasım 2022 Cumartesi tarihinde saat 19:58:47 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:

marioe911116

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Nov 19, 2022, 10:51:23 PM11/19/22
to gmx_MMPBSA
You must provide a topology file through -cp flag (assuming the topology file is named topol.top)

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

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