Problem with gmx_MMPBSA_ana

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Prabuddha Bhattacharya

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Feb 9, 2023, 10:37:17 AM2/9/23

to gmx_MMPBSA

Dear Sir

In my system, gmx_MMPBSA_ana is not running and showing an error related to matplotlib. However, this module was already installed in my system previously. Kindly find the screenshot for the same as the attached file.

Can you kindly help me to resolve this issue?

Thank you

Best regards

Prabuddha Bhattacharya

Screenshot from 2023-02-09 21-05-41.png

Mario Sergio Valdes

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Feb 9, 2023, 12:05:50 PM2/9/23

to gmx_MMPBSA

Could you show me the output of this command line?
conda list
Make sure the gmxMMPBSA environment is activated

Prabuddha Bhattacharya

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Feb 9, 2023, 12:44:31 PM2/9/23

to Mario Sergio Valdes, gmx_MMPBSA

Dear Sir

The gmxMMPBSA environment was activated using "conda activate gmxMMPBSA".

Kindly find the output log file as attachment. Please let me know if any other information or file is needed.

Thank you so much for your time,

Best regards

Prabuddha Bhattacharya

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gmx_MMPBSA.log

Mario Sergio Valdes

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Feb 9, 2023, 12:46:52 PM2/9/23

to gmx_MMPBSA

Please, show me the conda list command-line output

Prabuddha Bhattacharya

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Feb 9, 2023, 12:59:34 PM2/9/23

to Mario Sergio Valdes, gmx_MMPBSA

Dear Sir

Following is the conda list output :

(gmxMMPBSA) prabuddha@prabuddha:/media/prabuddha/New Volume3/MMPBSA_Final_check$ conda list
# packages in environment at /home/prabuddha/miniconda3/envs/gmxMMPBSA:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
ambertools 21.12 py39hc630cb1_0 conda-forge
amberutils 21.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
binutils 2.39 hdd6e379_1 conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_11 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.2.0 h7f98852_0 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
compilers 1.2.0 ha770c72_0 conda-forge
curl 7.86.0 h7bff187_1 conda-forge
cxx-compiler 1.2.0 h4bd325d_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.30 py39h5a03fae_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
fonttools 4.38.0 py39hb9d737c_1 conda-forge
fortran-compiler 1.2.0 h1990efc_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
gcc_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gcc_linux-64 9.5.0 h4258300_11 conda-forge
gfortran_impl_linux-64 9.5.0 hf1096a2_19 conda-forge
gfortran_linux-64 9.5.0 hdb51d14_11 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gmx-mmpbsa 1.5.7 pypi_0 pypi
gxx_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gxx_linux-64 9.5.0 h43f449f_11 conda-forge
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
icu 70.1 h27087fc_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9e h166bdaf_2 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.2 py39hf939315_1 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
libbrotlidec 1.0.9 h166bdaf_8 conda-forge
libbrotlienc 1.0.9 h166bdaf_8 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcurl 7.86.0 h7bff187_1 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h6a678d5_6
libgcc-devel_linux-64 9.5.0 h0a57e50_19 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
libnetcdf 4.8.1 nompi_h329d8a1_102 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libsanitizer 9.5.0 h2f262e1_19 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 9.5.0 h0a57e50_19 conda-forge
libstdcxx-ng 11.2.0 h1234567_1
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libzip 1.9.2 hc869a4a_1 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.1.3 py39h32b9844_3 conda-forge
mpich 4.0.2 h846660c_100 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.3 h5eee18b_3
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge
numpy 1.22.3 py39hc58783e_2 conda-forge
openjpeg 2.5.0 h7d73246_0 conda-forge
openssl 1.1.1s h0b41bf4_1 conda-forge
packaging 23.0 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.1rc0 pypi_0 pypi
pandas 1.4.2 py39h1832856_1 conda-forge
parmed 3.4.3+10.ga195c7e pypi_0 pypi
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.1.1 py39hae2aec6_1 conda-forge
pip 22.3.1 py39h06a4308_0
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyqt5 5.15.7 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi
python 3.9.16 h7a1cb2a_0
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2022.7.1 pyhd8ed1ab_0 conda-forge
readline 8.2 h5eee18b_0
sander 16.0 pypi_0 pypi
seaborn 0.11.2 pypi_0 pypi
setuptools 65.6.3 py39h06a4308_0
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.40.1 h5082296_0
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h1ccaba5_0
tqdm 4.64.1 pypi_0 pypi
tzdata 2022g h04d1e81_0
unicodedata2 15.0.0 py39hb9d737c_0 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.10 h5eee18b_1
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h8a70e8d_1 conda-forge

Please let me know if something else is needed.

Thank you

Best regards

Prabuddha Bhattacharya

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/2582c211-3dd2-4352-9c69-51d5c98729e6n%40googlegroups.com.

Mario Sergio Valdes

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Feb 9, 2023, 1:07:01 PM2/9/23

to gmx_MMPBSA

I don't see matplotlib here and seeing that you installed matplotlib on the system python, I suspect you have environment variables defined pointing there. If possible, show me your environment variables (for security, you can send me this information to my personal mail).

Execute the following command:

env

Mario Sergio Valdes

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Feb 9, 2023, 1:26:32 PM2/9/23

to gmx_MMPBSA

I see. You have defined the PYTHONPATH variable. That conflicts with the conda environment since those libraries are used and not updated according to dependencies.
I describe the solution in this comment (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/208#issuecomment-1082089083). Since the current conda environment does not contain the necessary packages, it is recommended to perform environment generation and installation of all packages again, making sure that the PYTHONPATH variable was unset.
Note that defining the PYTHONPATH variable can generate conflicts with all the python versions you have installed in your system, so it is recommended not to set it.

Prabuddha Bhattacharya

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Feb 9, 2023, 1:35:04 PM2/9/23

to Mario Sergio Valdes, gmx_MMPBSA

Dear Sir

Can you please elaborate on the process that you are suggesting and help me to execute the same? I am not much aware of python programming.

Thank you so much again.

Best regards

Prabuddha Bhattacharya

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/67f57c81-47a8-49b1-97e4-f314eb9ab423n%40googlegroups.com.

Mario Sergio Valdes

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Feb 9, 2023, 2:17:51 PM2/9/23

to gmx_MMPBSA

Please, follow these instructions:

- Open a terminal
- Unset the PYTHONPATH variable
- run the installation of gmx_MMPBSA in an environment
- download the env.yml file (wget https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/env.yml)
- create the environment (conda conda env create -n gmxMMPBSA --file env.yml)
- activate the environment (conda activate gmxMMPBSA)
You should be able to run gmx_MMPBSA_ana without any problems.
My recommendation is to remove the PYTHONPATH variable definition from your .bashrc. However, if you really need it, then you can do the following to avoid the package conflict:
- open the ~/.bashrc file
- define an alias for the activation environment
- alias act_gmxMMPBSA="source /home/mario/programs/gromacs2021.5/bin/GMXRC; export LD_LIBRARY_PATH=/home/mario/programs/miniconda3/envs/gmxMMPBSA/lib; conda activate gmxMMPBSA; unset PYTHONPATH"

This alias does the following (for the current session only):

Activates Gromacs 2021.5.
Exports LD_LIBRARY_PATH to use modern conda libraries instead of Centos7 libraries.
Activates the conda environment gmxMMPBSA
And unset the PYTHONPATH variable to avoid package conflicts

To remove any of these definitions, you only need to remove them from the alias. For instance,

alias act_gmxMMPBSA="conda activate gmxMMPBSA; unset PYTHONPATH"

In this case, the alias only activates the gmxMMPBSA conda environment and unset PYTHONPATH

Finally, to execute it, you must save the .bashrc file, open a new terminal and execute the name of the alias. For example:

mario@mario-LabPC:~$ act_gmxMMPBSA

You should see the prompt change to (gmxMMPBSA)mario@mario-LabPC:~$

Let me know if works for you

Prabuddha Bhattacharya

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Feb 9, 2023, 2:24:29 PM2/9/23

to Mario Sergio Valdes, gmx_MMPBSA

Thank you so much sir. I will try doing it according to your instructions and get back to you as soon as possible.

Best regards

To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/2e6b0d93-ccc7-41f3-ada0-4e88bbf2d7bcn%40googlegroups.com.

Prabuddha Bhattacharya

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Feb 9, 2023, 4:21:02 PM2/9/23

to Mario Sergio Valdes, gmx_MMPBSA

Dear Sir

I did the following:

- opened the ~/.bashrc file
- defined an alias for the activation environment
- alias act_gmxMMPBSA="export LD_LIBRARY_PATH=/home/mario/programs/miniconda3/envs/gmxMMPBSA/lib; conda activate gmxMMPBSA; unset PYTHONPATH".
Saved the .bashrc file, opened a new terminal and executed the name of the alias.

Upon trying to run the gmx_MMPBSA_ana, got the following error-

ModuleNotFoundError: No module named 'scipy'

So I tried to reinstall the python libraries using the command - conda install -c conda-forge sklearn-pandas scipy matplotlib

This last command for the installation of python libraries got executed without any error. The conda list now shows the following packages:

# packages in environment at /home/prabuddha/miniconda3/envs/gmxMMPBSA:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge

alsa-lib 1.2.8 h166bdaf_0 conda-forge

ambertools 21.12 py39hc630cb1_0 conda-forge
amberutils 21.0 pypi_0 pypi

appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge

binutils 2.39 hdd6e379_1 conda-forge
binutils_impl_linux-64 2.39 he00db2b_1 conda-forge
binutils_linux-64 2.39 h5fc0e48_11 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge

brotlipy 0.7.0 py39hb9d737c_1005 conda-forge

bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.2.0 h7f98852_0 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge

cffi 1.15.1 py39he91dace_3 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
compilers 1.2.0 ha770c72_0 conda-forge
contourpy 1.0.7 py39h4b4f3f3_0 conda-forge
cryptography 38.0.4 py39hd97740a_0 conda-forge

curl 7.86.0 h7bff187_1 conda-forge
cxx-compiler 1.2.0 h4bd325d_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.30 py39h5a03fae_0 conda-forge

dbus 1.13.6 h5008d03_3 conda-forge
expat 2.5.0 h27087fc_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge

fonttools 4.38.0 py39hb9d737c_1 conda-forge
fortran-compiler 1.2.0 h1990efc_0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
gcc_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gcc_linux-64 9.5.0 h4258300_11 conda-forge

gettext 0.21.1 h27087fc_0 conda-forge

gfortran_impl_linux-64 9.5.0 hf1096a2_19 conda-forge
gfortran_linux-64 9.5.0 hdb51d14_11 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge

glib 2.74.1 h6239696_1 conda-forge
glib-tools 2.74.1 h6239696_1 conda-forge
gmx-mmpbsa 1.5.7 pypi_0 pypi
gst-plugins-base 1.21.3 h4243ec0_1 conda-forge
gstreamer 1.21.3 h25f0c4b_1 conda-forge
gstreamer-orc 0.4.33 h166bdaf_0 conda-forge

gxx_impl_linux-64 9.5.0 h99780fb_19 conda-forge
gxx_linux-64 9.5.0 h43f449f_11 conda-forge
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h2386368_104 conda-forge
icu 70.1 h27087fc_0 conda-forge

idna 3.4 pyhd8ed1ab_0 conda-forge
jack 1.9.22 h11f4161_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
joblib 1.2.0 pyhd8ed1ab_0 conda-forge

jpeg 9e h166bdaf_2 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.2 py39hf939315_1 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge

lame 3.100 h166bdaf_1003 conda-forge

lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
libbrotlidec 1.0.9 h166bdaf_8 conda-forge
libbrotlienc 1.0.9 h166bdaf_8 conda-forge

libcap 2.66 ha37c62d_0 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libclang 15.0.7 default_had23c3d_1 conda-forge
libclang13 15.0.7 default_h3e3d535_1 conda-forge
libcups 2.3.3 h3e49a29_2 conda-forge
libcurl 7.86.0 h7bff187_1 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge

libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge

libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h6a678d5_6
libflac 1.4.2 h27087fc_0 conda-forge

libgcc-devel_linux-64 9.5.0 h0a57e50_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge

libgcrypt 1.10.1 h166bdaf_0 conda-forge

libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge

libglib 2.74.1 h606061b_1 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libgpg-error 1.46 h620e276_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libllvm15 15.0.7 hadd5161_0 conda-forge

libnetcdf 4.8.1 nompi_h329d8a1_102 conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge

libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libpq 14.5 h72a31a5_3 conda-forge
libsanitizer 9.5.0 h2f262e1_19 conda-forge
libsndfile 1.2.0 hb75c966_0 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge

libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 9.5.0 h0a57e50_19 conda-forge

libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libsystemd0 252 h2a991cd_0 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libtool 2.4.7 h27087fc_0 conda-forge
libudev1 252 h166bdaf_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge

libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge

libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.10.3 h7463322_0 conda-forge

libzip 1.9.2 hc869a4a_1 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge

matplotlib 3.6.3 py39hf3d152e_0 conda-forge
matplotlib-base 3.6.3 py39he190548_0 conda-forge
mpg123 1.31.2 hcb278e6_0 conda-forge

mpi 1.0 mpich conda-forge
mpi4py 3.1.3 py39h32b9844_3 conda-forge
mpich 4.0.2 h846660c_100 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge

mysql-common 8.0.32 h14678bc_0 conda-forge
mysql-libs 8.0.32 h54cf53e_0 conda-forge

ncurses 6.3 h5eee18b_3
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge

nspr 4.35 h27087fc_0 conda-forge
nss 3.82 he02c5a1_0 conda-forge

numpy 1.22.3 py39hc58783e_2 conda-forge
openjpeg 2.5.0 h7d73246_0 conda-forge
openssl 1.1.1s h0b41bf4_1 conda-forge
packaging 23.0 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.1rc0 pypi_0 pypi
pandas 1.4.2 py39h1832856_1 conda-forge
parmed 3.4.3+10.ga195c7e pypi_0 pypi

pcre2 10.40 hc3806b6_0 conda-forge

perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.1.1 py39hae2aec6_1 conda-forge
pip 22.3.1 py39h06a4308_0

ply 3.11 py_1 conda-forge
pooch 1.6.0 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pulseaudio 16.1 h4ab2085_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyqt 5.15.7 py39h5c7b992_3 conda-forge

pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi

pysocks 1.7.1 pyha2e5f31_6 conda-forge

python 3.9.16 h7a1cb2a_0
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2022.7.1 pyhd8ed1ab_0 conda-forge

qt-main 5.15.6 h7acdfc8_2 conda-forge
readline 8.2 h5eee18b_0
requests 2.28.2 pyhd8ed1ab_0 conda-forge
sander 16.0 pypi_0 pypi
scikit-learn 1.2.1 py39h86b2a18_0 conda-forge
scipy 1.10.0 py39h7360e5f_2 conda-forge

seaborn 0.11.2 pypi_0 pypi
setuptools 65.6.3 py39h06a4308_0

sip 6.7.7 py39h227be39_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sklearn-pandas 2.2.0 pyhd8ed1ab_0 conda-forge

sqlite 3.40.1 h5082296_0
sysroot_linux-64 2.12 he073ed8_15 conda-forge

threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tk 8.6.12 h1ccaba5_0
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tornado 6.2 py39hb9d737c_1 conda-forge

tqdm 4.64.1 pypi_0 pypi
tzdata 2022g h04d1e81_0
unicodedata2 15.0.0 py39hb9d737c_0 conda-forge

urllib3 1.26.14 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge

xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.10 h5eee18b_1
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h8a70e8d_1 conda-forge

The matplotlib and scipy seem to be there in this list.

However, upon trying to run the gmx_MMPBSA_ana, now I got the following error-

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.
Aborted (core dumped)

Did I commit any mistake in the process?

Best regards

Prabuddha Bhattacharya

Mario Sergio Valdes

unread,

Feb 9, 2023, 4:27:37 PM2/9/23

to gmx_MMPBSA

Please, check this info:

- https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/OS_issues/#solution_2

- https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/208#issuecomment-1082037051

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