Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20

From: Ray Luo <rluo.uci.edu>
Date: Tue, 15 Dec 2020 10:23:59 -0800

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

Received on Tue Dec 15 2020 - 10:30:02 PST