As your error messages suggest, you are having an issue importing the
parmed program within Amber. This is likely because 1) parmed is not
installed properly or 2) you are sourcing/using a different version of
python than the one used to compile Amber (most likely problem). I'm
guessing you need to set your PYTHONPATH variable to point to the proper
python version to fix this issue.
Hope that helps.
-Bill
On Tue, Apr 2, 2024 at 7:23 PM ABDELATIF MESSAOUDI via AMBER <
amber.ambermd.org> wrote:
> Dear Amber Users
> I am running AMBER MMGGSA
>
> mpirun -np 8 /home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py -O -i
> mmgbsa.in
> -o FINAL_RESULTS_MMPBSA.dat -sp SKtop -cp SKnosolv.top -rp receptor.top -lp
> ligand.top -y SK_c.mdcrd -do FINAL_DECOMP_MMPBSA.dat -eo
> FINAL_NRJ_TERMS.csv -deo FINAL_DECOMP_NRJ.csv > progress.log &
>
> I am getting an error message that mentions:
>
> base) lcmvar.lcmvar-System-Version:~/+Abdel/SQ_tmp/+Analyse$ mpirun -np 8
> /home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py -O -i mmgbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp SKtop -cp SKnosolv.top -rp receptor.top -lp
> ligand.top -y SK_c.mdcrd -do FINAL_DECOMP_MMPBSA.dat -eo
> FINAL_NRJ_TERMS.csv -deo FINAL_DECOMP_NRJ.csv > progress.log &
> [1] 7301
> (base) lcmvar.lcmvar-System-Version:~/+Abdel/SQ_tmp/+Analyse$ 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
> --------------------------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --------------------------------------------------------------------------
> 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)
> --------------------------------------------------------------------------
> 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: [[32390,1],0]
> Exit code: 1
> --------------------------------------------------------------------------
>
> [1]+ Termine 1 mpirun -np 8
> /home/lcmvar/SOFT/amber23/amber22/bin/MMPBSA.py -O -i mmgbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp SKtop -cp SKnosolv.top -rp receptor.top -lp
> ligand.top -y SK_c.mdcrd -do FINAL_DECOMP_MMPBSA.dat -eo
> FINAL_NRJ_TERMS.csv -deo FINAL_DECOMP_NRJ.csv > progress.log
> (base) lcmvar.lcmvar-System-Version:~/+Abdel/SQ_tmp/+Analyse$
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Tue Apr 02 2024 - 23:30:02 PDT
