Dear Ray,
Thank you for your reply. I already sourced the following file, I still get
error.
Traceback (most recent call last):
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/__init__.py",
line 25, in <module>
from simtk.unit import *
ModuleNotFoundError: No module named 'simtk'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/bin/MMPBSA.py.MPI",
line 41, in <module>
from MMPBSA_mods import main
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/MMPBSA_mods/main.py",
line 43, in <module>
from MMPBSA_mods.createinput import create_inputs
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/MMPBSA_mods/createinput.py",
line 43, in <module>
from parmed.amber.mdin import Mdin
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/__init__.py",
line 22, in <module>
from parmed import unit, utils
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/__init__.py",
line 27, in <module>
from parmed.unit.unit import Unit, is_unit
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/unit/unit.py",
line 35, in <module>
from parmed.utils.six import iterkeys
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/utils/__init__.py",
line 3, in <module>
from parmed.utils.pairlist import find_atom_pairs
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/lib/python3.6/site-packages/ParmEd-3.0.0+57.g74a84d30-py3.6-linux-x86_64.egg/parmed/utils/pairlist.py",
line 5, in <module>
import numpy as np
ModuleNotFoundError: No module named 'numpy'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/bin/MMPBSA.py.MPI",
line 48, in <module>
(amberhome, amberhome))
ImportError: Could not import Amber Python modules. Please make sure you
have sourced /cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/amber.sh
(if you are using sh/ksh/bash/zsh) or /cvmfs/
restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda9.0/openmpi2.1/amber/18/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: [[35435,1],0]
Exit code: 1
--------------------------------------------------------------------------
Best regards,
Rui
On Thu, Jan 2, 2020 at 11:16 PM Ray Luo <rluo.uci.edu> wrote:
> Please change the line to:
> istrng=0.150, radipot=0
>
> There are extra * in the line.
>
> All the best,
> Ray
>
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical Physics, Biomedical Engineering, and Chemical Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Thu, Jan 2, 2020 at 9:38 PM Rui Chen <rchen6.ualberta.ca> wrote:
> >
> > Dear Ray,
> >
> > I changed the input file to:
> > Input file for running GB & PB
> > &general
> > startframe=7000, endframe=7500, interval=100, keep_files=0,
> > /
> > &gb
> >
> > igb=8,
> >
> > saltcon=0.150, *radipot=0,* surften=0.0072,
> >
> >
> > surfoff=0.0, molsurf=0,
> > /
> > &pb
> > istrng=0.150, *radipot=0,*
> > /
> >
> > I got the following error:
> > InputError: Unknown variable radipot in &gb
> > Enter `MMPBSA.py.MPI --help` for help
> > -------------------------------------------------------
> > 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: [[31708,1],0]
> > Exit code: 1
> >
> > By the way, I used Amber/16 (the newest version) in our local cluster to
> > calculate the binding free energy. Should I use other clusters and maybe
> > the newest version of Amber?
> >
> > Best regards,
> > Rui
> >
> > On Thu, Jan 2, 2020 at 5:38 PM Ray Luo <rluo.uci.edu> wrote:
> >
> > > Hi Rui,
> > >
> > > I think you are probably using one of the earlier versions that set
> > > radiopt=1 by default. Please set "radipot=0" after "istrng=0.150," in
> > > your input file and you should be good to go.
> > >
> > > All the best,
> > > Ray
> > > --
> > > Ray Luo, Ph.D.
> > > Professor of Structural Biology/Biochemistry/Biophysics,
> > > Chemical Physics, Biomedical Engineering, and Chemical Engineering
> > > Department of Molecular Biology and Biochemistry
> > > University of California, Irvine, CA 92697-3900
> > >
> > > On Thu, Jan 2, 2020 at 4:29 PM Rui Chen <rchen6.ualberta.ca> wrote:
> > > >
> > > > Hello,
> > > >
> > > > I am running MMPBSA for the first time using the following script:
> > > (because
> > > > I only want to check if the script works or not, so I specified large
> > > > interval, so that I can get results in 5 min)
> > > > Input file for running GB & PB
> > > > &general
> > > > startframe=7000, endframe=7500, interval=100, keep_files=0,
> > > > /
> > > > &gb
> > > >
> > > > igb=8,
> > > >
> > > > saltcon=0.150, surften=0.0072,
> > > >
> > > > surfoff=0.0, molsurf=0,
> > > > /
> > > > &pb
> > > > istrng=0.150,
> > > > /
> > > >
> > > > I got the following error when I run PBSA and GBSA together:
> CalcError:
> > > > /cm/shared/apps/amber16/bin/mmpbsa_py_energy failed with prmtop
> > > com.prmtop!
> > > > PB Bomb in pb_aaradi(): No radius assigned for atom 6615 C1 Cg
> > > >
> > > > When I run GBSA alone, I got a different error:
> > > > IOError: [Errno 2] No such file or directory:
> > > > '_MMPBSA_complex_gb_surf.dat.0'
> > > >
> > > > How can I solve the problem? Looking forward to your reply.
> > > >
> > > > Best regards,
> > > > Rui
> > > > _______________________________________________
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> > >
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Received on Fri Jan 03 2020 - 09:00:01 PST
