PyMOL Installation In Centos 7

Varsha Achuthan

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Mar 16, 2023, 2:20:37 AM3/16/23

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Hi all,

I have installed gmx_MMPBSA in my system and it is working fine.

As the decomposition analysis has an output that can be viewed in PyMOL, I have installed PyMOL in the conda enviroment.

But then when gmx_MMPBSA_ana was run, I received the following error.

Can you help me fix this.

ERROR:root:MMPBSA_Error Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed. Check the gmx_MMPBSA.log file to report the problem.

log file screenshot.

Mario Sergio Valdes

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Mar 16, 2023, 2:27:39 AM3/16/23

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Are you using Centos in an HPC or as Desktop OS? The HPC OS commonly disabled the graphical drivers, so they don't support GUIs. However, you can copy the folder or the compact file to your PC and then analyze the result. To void this error output in the HPC, you can use the -nogui flag.

Varsha Achuthan

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Mar 16, 2023, 4:57:38 AM3/16/23

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Thankyou for the response Sir.

I am using Centos as a desktop OS.

Mario Sergio Valdes

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Mar 16, 2023, 5:24:43 AM3/16/23

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Please, check if you have PyQt installed:

python -m pip list

or

conda list

Varsha Achuthan

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Mar 16, 2023, 6:15:22 AM3/16/23

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yes, all the necessary installation has been done correctly including the PyQt file.

when PyMol was added to the Conda environment, gmx_MMPBSA_ana didn't open.

It was working fine until then.

Mario Sergio Valdes

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Mar 16, 2023, 1:06:02 PM3/16/23

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Please, show the conda packages list (conda list)

Can you check is this solution works for you (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/208)?

Varsha Achuthan

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Mar 17, 2023, 6:10:12 AM3/17/23

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conda list:-

# packages in environment at /home/guest/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
brotlipy 0.7.0 py310h5764c6d_1005 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h255011f_3 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
conda 23.1.0 py310hff52083_0 conda-forge
conda-content-trust 0.1.3 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.0.2 pyh38be061_0 conda-forge
conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge
cryptography 39.0.2 py310h34c0648_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.24.2 py310h8deb116_0 conda-forge
openssl 3.0.8 h0b41bf4_0 conda-forge
pandas 1.5.3 py310h9b08913_0 conda-forge
parmed 4.0.0 py310heca2aa9_0 conda-forge
pip 23.0.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
pycosat 0.6.4 py310h5764c6d_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge
pyqt5 5.15.9 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.1 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.9 he550d4f_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.10 3_cp310 conda-forge
pytz 2022.7.1 pyhd8ed1ab_0 conda-forge
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.2 pyhd8ed1ab_0 conda-forge
ruamel.yaml 0.17.21 py310h1fa729e_3 conda-forge
ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge
setuptools 67.6.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
tzdata 2022g h191b570_0 conda-forge
urllib3 1.26.15 pyhd8ed1ab_0 conda-forge
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zstandard 0.19.0 py310hdeb6495_1 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge

Mario Sergio Valdes

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Mar 17, 2023, 5:19:51 PM3/17/23

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It seems that everything is normal. Please, try executing gmx_MMPBSA_ana and show me the output

Varsha Achuthan

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Mar 18, 2023, 6:17:30 AM3/18/23

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It is the same as I had sent in the first message.

I feel having PyMol and gmx_MMPSA in the same environment is not working.

And for now,I reinstalled gmx_MMPBSA_ana without PyMol in an other environment.Hence I am able to view the ana results but the PyMol results are not coming.

can you help me with this.

Mario Sergio Valdes

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Mar 18, 2023, 12:14:15 PM3/18/23

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I think that the problem is the pymol-open-source dependencies. After installing it, gmx_MMPBSA_ana not working. To fix it, I force to reinstall pyqt5 as follows:
python -m pip install pyqt5 -U --force
After that, pymol runs smoothly

Let me know if this works for you

Varsha Achuthan

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Mar 20, 2023, 5:50:54 AM3/20/23

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This worked!

Thankyou so much.

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