Abdelatif,
As Professor Case and others have stated (if I might be allowed some
editorial leeway), you keep sending in lengthy copypasta containing nothing
but error messages: this is not an effective way for you to get assistance.
It is painfully obvious that parmed is either not installed on your machine
or installed in a place not included in your PATH environment variable; and
your python distribution is 3.12, which is not going to fly.
Finally, have you actually added a line to your .bashrc to source amber.sh?
It looks to me like you haven't.
Unfortunately, until you make some progress on the self-help issues, your
installation will remain broken and that precludes doing anything, much
less a tutorial.
Cheers,
Todd
On Thu, Apr 4, 2024 at 7:49 PM ABDELATIF MESSAOUDI via AMBER <
amber.ambermd.org> wrote:
> Dear AMBER users,
> *I'am trying to follow tutorial in :*
> https://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm
>
> I am running Amber MMPBSA
> mpirun -np 8 /home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py -O -i
> mmpbsa.in
> -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop
> -rp ras.prmtop -lp raf.prmtop -y *.mdcrd
>
> (base) lcmvar.lcmvar-System-Version
> :~/+Abdel/SQ_tmp/temp_MMPPP/ras-raf_top_mdcrd$
> source $AMBERHOME/amber.sh
> (base) lcmvar.lcmvar-System-Version
> :~/+Abdel/SQ_tmp/temp_MMPPP/ras-raf_top_mdcrd$
> mpirun -np 8 /home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py -O -i
> mmpbsa.in
> -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop
> -rp ras.prmtop -lp raf.prmtop -y *.mdcrd &
> [1] 10962
> (base) lcmvar.lcmvar-System-Version
> :~/+Abdel/SQ_tmp/temp_MMPPP/ras-raf_top_mdcrd$
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 41, in
> <module>
> from MMPBSA_mods import main
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> line 44, in <module>
> from MMPBSA_mods.createinput import create_inputs
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/createinput.py",
> line 43, in <module>
> from parmed.amber.mdin import Mdin
> ModuleNotFoundError: No module named 'parmed'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 45, in
> <module>
> raise ImportError('Could not import Amber Python modules. Please make
> sure '
> ImportError: Could not import Amber Python modules. Please make sure you
> have sourced /home/lcmvar/SOFT/amber23/amber22/amber.sh (if you are using
> sh/ksh/bash/zsh) or /home/lcmvar/SOFT/amber23/amber22/amber.csh (if you are
> using csh/tcsh)
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 41, in
> <module>
> from MMPBSA_mods import main
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> line 44, in <module>
> from MMPBSA_mods.createinput import create_inputs
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/createinput.py",
> line 43, in <module>
> from parmed.amber.mdin import Mdin
> ModuleNotFoundError: No module named 'parmed'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 45, in
> <module>
> raise ImportError('Could not import Amber Python modules. Please make
> sure '
> ImportError: Could not import Amber Python modules. Please make sure you
> have sourced /home/lcmvar/SOFT/amber23/amber22/amber.sh (if you are using
> sh/ksh/bash/zsh) or /home/lcmvar/SOFT/amber23/amber22/amber.csh (if you are
> using csh/tcsh)
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 41, in
> <module>
> from MMPBSA_mods import main
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> line 44, in <module>
> from MMPBSA_mods.createinput import create_inputs
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/createinput.py",
> line 43, in <module>
> from parmed.amber.mdin import Mdin
> ModuleNotFoundError: No module named 'parmed'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 45, in
> <module>
> raise ImportError('Could not import Amber Python modules. Please make
> sure '
> ImportError: Could not import Amber Python modules. Please make sure you
> have sourced /home/lcmvar/SOFT/amber23/amber22/amber.sh (if you are using
> sh/ksh/bash/zsh) or /home/lcmvar/SOFT/amber23/amber22/amber.csh (if you are
> using csh/tcsh)
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 41, in
> <module>
> from MMPBSA_mods import main
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> line 44, in <module>
> from MMPBSA_mods.createinput import create_inputs
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/createinput.py",
> line 43, in <module>
> from parmed.amber.mdin import Mdin
> ModuleNotFoundError: No module named 'parmed'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 45, in
> <module>
> raise ImportError('Could not import Amber Python modules. Please make
> sure '
> ImportError: Could not import Amber Python modules. Please make sure you
> have sourced /home/lcmvar/SOFT/amber23/amber22/amber.sh (if you are using
> sh/ksh/bash/zsh) or /home/lcmvar/SOFT/amber23/amber22/amber.csh (if you are
> using csh/tcsh)
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 41, in
> <module>
> from MMPBSA_mods import main
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/main.py",
> line 44, in <module>
> from MMPBSA_mods.createinput import create_inputs
> File
>
> "/home/lcmvar/SOFT/amber23/amber22/lib/python3.12/site-packages/MMPBSA_mods/createinput.py",
> line 43, in <module>
> from parmed.amber.mdin import Mdin
> ModuleNotFoundError: No module named 'parmed'
>
> During handling of the above exception, another exception occurred:
>
> Traceback (most recent call last):
> File "/home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py", line 45, in
> <module>
> raise ImportError('Could not import Amber Python modules. Please make
> sure '
> ImportError: Could not import Amber Python modules. Please make sure you
> have sourced /home/lcmvar/SOFT/amber23/amber22/amber.sh (if you are using
> sh/ksh/bash/zsh) or /home/lcmvar/SOFT/amber23/amber22/amber.csh (if you are
> using csh/tcsh)
> --------------------------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
> Process name: [[18641,1],0]
> Exit code: 1
> -------------------------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 05 2024 - 06:00:02 PDT
