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-- 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 > > > > > _______________________________________________ > > > > > 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 > > > > > > > _______________________________________________ > > > 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 > > > _______________________________________________ > 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/amberReceived on Fri Jan 03 2020 - 12:30:02 PST