Dear All,
I'm trying to run MMPBSA.py.MPI using recently installed Amber20 for which
I sourced the amber.sh file from amber20 directory.
But I'm getting the following error which doesn't appear with the serial
version.
Do I need to change the .bashrc for this to work?
thanks in advance for your suggestions.
best regards
(base) [exx.c107739 mmpbsa-6701-tyr]$ echo $AMBERHOME
/home/exx/Downloads/amber20
(base) [exx.c107739 mmpbsa-6701-tyr]$ mpirun -np 12 MMPBSA.py.MPI -O -i
mmpbsa-decomp.in -o mmpbs-rouf-6701-tyr-pb.dat -do
decomp-rouf-6701-tyr-pb.dat -sp ../rouf-6701-tyr-solv.prmtop -cp
../rouf-6701-tyr-dry.prmtop -lp ../tyr-dry.prmtop -y ../
rouf-6701-tyr-solv-prod300.nc -rp ../rouf-6701-nolig-dry.prmtop
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
(base) [exx.c107739 mmpbsa-6701-tyr]$
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Tue Dec 15 2020 - 09:30:02 PST
