Errors using gmx_MMPBSA v.1.5

[gagandeep singh]

Dear gmx_MMPBSA team and users,

I am facing some errors when running the analysis using gmx_MMPBSA_ana with v1.5 on previous version runs as well as errors on running the calculation with v1.5.

On running gmx_MMPBSA_ana -f of v1.5 with previous version files, it gives the error:

Traceback (most recent call last):
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/analyzer/dialogs.py", line 359, in get_data
    self.parent.read_data(queue, self.options)
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/analyzer/gui.py", line 981, in read_data
    gmx_mmpbsa_api.load_file(path)
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/API.py", line 78, in load_file
    self._get_fromApp(fname)
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/API.py", line 368, in _get_fromApp
    app.parse_output_files()
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/main.py", line 977, in parse_output_files
    if self.INPUT['c2_entropy']:
KeyError: 'c2_entropy'
Aborted

While on running the calculations from scratch using v1.5, i get the following errors during compilation of entropy calculations step:

Beginning nmode calculations with /home/gsk/anaconda3/envs/gmxMMPBSA/bin/mmpbsa_py_nabnmode
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] Parsing results to output files...

  File "/home/gsk/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 33, in <module>
    sys.exit(load_entry_point('gmx-MMPBSA==0+unknown', 'console_scripts', 'gmx_MMPBSA')())
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/app.py", line 112, in gmxmmpbsa
    app.parse_output_files()
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/main.py", line 998, in parse_output_files
    self.calc_types.normal[key]['delta'] = BindingStatistics(self.calc_types.normal[key]['complex'],
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/amber_outputs.py", line 838, in __init__
    self._delta()
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/gmx_MMPBSA-0+unknown-py3.9.egg/GMXMMPBSA/amber_outputs.py", line 855, in _delta
    diff = self.com[key] - self.rec[key] - self.lig[key]
KeyError: 'BOND'
Exiting. All files have been retained.

Kindly help to resolve the problem.

Thanks and Regards,

Gagandeep Singh

--

Assistant Research Officer (Biotechnology)

Central Ayurveda Research Institute, Jhansi

Ph.D. Scholar

KSBS, IIT Delhi

Mob- 8178163366, 8285477478

[Mario Sergio Valdes]

Unfortunately, the current version is not compatible with previous versions, at least not officially due to the large number of changes that were introduced. However, modifying the _GMXMMPBSA_info file could open the results in gmx_MMPBSA_ana. This would take a considerable amount of time and rehearsal.
To do this, you would have to make sure that all the variables defined in the *_info of version 1.5.x are in their previous *_info. And as you can see, the number of variables in the current version has increased dramatically.

In the second part, I think it's a bug, I'm going to do the relevant tests. And I'll tell you as soon as I identify the problem.

Note: Please do not install gmx_MMPBSA using setup.py install as it does not allow you to get the development version (gmx_MMPBSA-0+unknown-py3.9.egg). Use python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U instead which does check the current version

[marioe911116]

In the new version v1.5.0.3, the bug has been corrected.

https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/releases/tag/v1.5.0.3

Please, upgrade to the new version with:

python -m pip install gmx_MMPBSA -U (if you installed with conda environment (pip))

or

amber.python -m pip install gmx_MMPBSA -U (if you installed with AmberTools compilation)

[gagandeep singh]

I am facing the error (terminal output attached) regarding mpi4py and GLIBC_2.14 library on running the update command using pip.

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[Mario Sergio Valdes]

Since you installed gmx_MMPBSA using setup.py install, as I recommended you not to do, you must remove the previous installation manually. pip doesn't know how to handle installations made with setup.py, so you won't be able to update it this way. Once you manually uninstall gmx_MMPBSA, then install mpi4py from conda (conda install -c conda-forge mpi4py) and then gmx_MMPBSA (python -m pip install gmx_MMPBSA)

[gagandeep singh]

I have started again from the scratch following the steps mentioned on your webpage (file attached) except i have separately installed ambertools and mpi4py as running tem in single conda command used to solve for hours. Still facing the mpi4py error.

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[Mario Sergio Valdes]

Now the problem is that conda is installed the mpi4py = 3.0.3, while gmx_MMPBSA tries to install the mpi4py = 3.1.3. 

Please, remove the installed packages (ambertools and compilers) since the install mpi4py after they end in error

conda remove ambertools compilers -y

Please, force conda to install the mpi4py = 3.1.3

conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y

python -m pip install gmx-mmpbsa

Let me know any problem

Mario S.

[gagandeep singh]

The installation went all after the previous suggestion.

However i did a test run for enthalpic contribution for only 11 frames of Protein-ligand and on the analysis part, the gmx_MMPBSA_ana crashes on clicking any of the analysis options with the GLIBCXX error:

[INFO   ] Opening gmx_MMPBSA_ana to analyze results...

/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py:1448: PerformanceWarning: indexing past lexsort depth may impact performance.
  new_data = self._remove_empty_terms(data[level][(level1,)])
/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py:1452: PerformanceWarning: indexing past lexsort depth may impact performance.
  if self._remove_empty_charts(data[level][(level1, level2)]):
/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py:1465: PerformanceWarning: indexing past lexsort depth may impact performance.
  temp_dat = data[level][(level1, level2)]
/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py:1473: PerformanceWarning: indexing past lexsort depth may impact performance.
  temp_dat = data[level][(level1, level2, level3)]

Traceback (most recent call last):

  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/customitem.py", line 322, in fn_btn_group
    self.plotting_line(checked)
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/customitem.py", line 333, in plotting_line
    from GMXMMPBSA.analyzer.plots import LineChart
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/plots.py", line 24, in <module>
    import seaborn as sns
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/__init__.py", line 2, in <module>
    from .rcmod import *  # noqa: F401,F403
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/rcmod.py", line 7, in <module>
    from . import palettes
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/palettes.py", line 9, in <module>
    from .utils import desaturate, get_color_cycle
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/utils.py", line 10, in <module>
    from scipy import stats
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/stats/__init__.py", line 453, in <module>
    from ._stats_py import *
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/stats/_stats_py.py", line 38, in <module>
    from scipy.spatial.distance import cdist
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/spatial/__init__.py", line 107, in <module>
    from ._procrustes import procrustes
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/spatial/_procrustes.py", line 9, in <module>
    from scipy.linalg import orthogonal_procrustes
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/linalg/__init__.py", line 210, in <module>
    from ._matfuncs import *
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/linalg/_matfuncs.py", line 21, in <module>
    from ._matfuncs_sqrtm import sqrtm
  File "/home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/linalg/_matfuncs_sqrtm.py", line 24, in <module>
    from ._matfuncs_sqrtm_triu import within_block_loop
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /home/gsk/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/linalg/_matfuncs_sqrtm_triu.cpython-39-x86_64-linux-gnu.so)
[ERROR  ] Unable to start gmx_MMPBSA_ana...
[INFO   ] Finalized...

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[Mario Sergio Valdes]

Try to install/update the libstdc++

sudo apt  install libstdc++6

[gagandeep singh]

libstdc++6 is already the newest version (5.4.0-6ubuntu1~16.04.12).

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[Mario Sergio Valdes]

Are you using ubuntu 16.04? It seems that there are some problems with this library. Please follow the instructions here (https://stackoverflow.com/questions/48453497/anaconda-libstdc-so-6-version-glibcxx-3-4-20-not-found) and tell me if you solved it.

[gagandeep singh]

Yes, I am using ubuntu 16.04.

None of the solutions given in the attached thread worked.

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[Mario Ernesto]

We haven't tested the new version on Ubuntu 16.04... Let us do some tests and get back to you...

cheers!

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[gagandeep singh]

Ok, Thanks.

Gagandeep Singh
Assistant Research Officer (Biotechnology),

CARI,Jhansi,
Ministry of AYUSH

[Mario Sergio Valdes]

Try with these instructions

Check the supported versions

strings/usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX

Add this repo and update the libstdc++6 library

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt update
sudo apt install gcc-4.9
sudo apt install upgrade libstdc++6

Check the supported versions again 

strings/usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX

This should solve the problem.

Consider upgrading to a more recent OS, Ubuntu 16.04 is outdated since 2021. This will be one of the few times that we will support the outdated OS, since solving these problems requires a considerable amount of time, which we do not have. We only support "old" OS if they are HPC, as these are not easily upgradeable, but are usually backed up by staff experienced in resolving similar bugs.

HTH!

Mario S.

[gagandeep singh]

Thank a lot for your support. It worked.

Regards

Gagandeep Singh
Assistant Research Officer (Biotechnology),

CARI,Jhansi,
Ministry of AYUSH

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