Dear All,
As suggested I added the "source /home/exx/Downloads/amber20/amber.sh" into
my .bashrc file then sourced it.
But I'm still getting error messages that amber18 is in the path. I'm
curious to understand why this error didn't show up while testing the
parallel version but appears while trying to use MMPBSA.py.MPI command.
Can you please suggest me what is the best method to have two different
versions of amber of a workstation and call a specific one when required?
Thank you in advance and best regards.
P.S. My .bashrc didn't even mention amber18 at any time, thus not sure how
it was set up by the Exxact team who configured/installed amber18 on this
GPU system.
(base) [exx.c107739 mmpbsa-6701-tyr]$ source
/home/exx/Downloads/amber20/amber.sh
(base) [exx.c107739 mmpbsa-6701-tyr]$ echo $AMBERHOME
/home/exx/Downloads/amber20
(base) [exx.c107739 mmpbsa-6701-tyr]$ vim /home/exx/.bashrc
(base) [exx.c107739 mmpbsa-6701-tyr]$ source /home/exx/.bashrc
(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 -lp ../tyr-dry.prmtop -y ../rouf-6701-tyr-solv-prod300.nc
-rp ../rouf-6701-nolig-dry.prmtop
Traceback (most recent call last):
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>
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)
Traceback (most recent
call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
^
SyntaxError: invalid syntax
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>
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 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)
from MMPBSA_mods.amber_outputs import (QHout,
NMODEout, QMMMout, GBout, PBout,
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/amber_outputs.py",
line 586
print('Not all frames minimized within tolerance', file=sys.stderr)
from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
^
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 ^
SyntaxError
print('Not all frames minimized within tolerance', file=sys.stderr)
: invalid syntax
^
SyntaxError: invalid syntax
Traceback (most recent call last):
from MMPBSA_mods.amber_outputs import (QHout, NMODEout, QMMMout, GBout,
PBout,
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/amber_outputs.py",
line from MMPBSA_mods import main
File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
586
print('Not all frames minimized within tolerance', file=sys.stderr)
Traceback (most recent call last):
File "/usr/local/amber18/bin/MMPBSA.py.MPI", line 41, in <module>
from MMPBSA_mods
import main
^
SyntaxError: File
"/home/exx/Downloads/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 34, in <module>
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)
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
Traceback (most recent call last):
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)
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>
^
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
^
SyntaxError: invalid syntax
586
print('Not all frames minimized within tolerance', file=sys.stderr)
^
SyntaxError: invalid syntax
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]$
On Tue, Dec 15, 2020 at 11:54 PM Ray Luo <rluo.uci.edu> wrote:
> Yes, you do need to change .bashrc. Looks like amber18 is ahead of
> amber20 in your path.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Tue, Dec 15, 2020 at 9:26 AM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
> >
> > 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
> >
> > P Please consider the environment before printing this e-mail
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
P Please consider the environment before printing this e-mail
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Received on Tue Dec 15 2020 - 18:30:03 PST
