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
-------------------------------------------------------------------------
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Received on Thu Apr 04 2024 - 18:00:02 PDT
