files.zip
<
https://drive.google.com/a/ualberta.ca/file/d/1ZCgOgTy5iU7vKXWrZt6pCEwy90v5wR1e/view?usp=drive_web>
Dear Ray,
Please find attached the files. Thank you.
Best regards,
Rui
On Fri, Jan 3, 2020 at 1:06 PM Ray Luo <rluo.uci.edu> wrote:
> Hi Rui,
>
> Just email me your input file OFF THE LIST and I'll get back to you.
>
> 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 Fri, Jan 3, 2020 at 9:00 AM Rui Chen <rchen6.ualberta.ca> wrote:
> >
> > 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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Received on Fri Jan 03 2020 - 13:00:01 PST
