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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 Thu, Mar 1, 2018 at 2:15 PM, Morrow,John Kenneth <JKMorrow.mdanderson.org> wrote: > Hi Ray, even with the serial version it is not working. My understanding is that amber17 is just amber16 with the latest ambertools? Is the difference between amber16 and 17 really that different in regards to MMPBSA? > > _______________________________________________ > > From: Ray Luo <rluo.uci.edu> > Date: Sun, 11 Feb 2018 17:40:18 -0800 > > Dear John, > > How about you first try the serial version of mmpbsa.py for a few > snapshots? If you are using radiopt=0 in amber17, this shouldn't > happen. > > 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 Sun, Feb 11, 2018 at 2:08 PM, Morrow,John Kenneth > <JKMorrow.mdanderson.org> wrote: > > -----Original Message----- > From: Morrow,John Kenneth [mailto:JKMorrow.mdanderson.org] > Sent: Saturday, January 27, 2018 8:04 AM > To: AMBER Mailing List <amber.ambermd.org> > Subject: Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C > > Hi Ray/Amber community, I have changed my script to include amber16, and have changed my radiopt to 0, but I am still getting a error that is similar but not identical (New error: PB bomb in pb_setgrd(): Allocation aborted). > > I have included below: > > 1. My .mdin file, > 2. My output, and > 3. My script i use to run MMPBSA > > Note: My mmpbsa.in file is the same as before (at bottom). Any help on this matter is appreciated. > > _MMPBSA_pb.mdin: > PB > npbopt = 0 > istrng = 150.0 > bcopt = 5 > inp = 2 > accept = 0.001 > cavity_offset = -0.5692 > maxitn = 1000 > fillratio = 4.0 > iprob = 2.0 > space = 0.5 > eneopt = 2 > dprob = 1.4 > radiopt = 0 > dbfopt = 1 > epsin = 1.0 > nfocus = 2 > cutnb = 0 > epsout = 80.0 > fscale = 8 > solvopt = 1 > smoothopt = 1 > sprob = 0.557 > cavity_surften = 0.0378 > > > > OUTPUT.1374128: > Currently Loaded Modules: > 1) TACC/1.0 3) cray_mpich/7.3.0 5) python/2.7.12 > 2) intel/16.0.1 4) amber/16.0 > > "DIR = /work/01936/jkmorrow/Skp2/docked557/Skp2_557docked.notail/mmpbsa/2nd.try_DS.and.Babel/" > Loading and checking parameter files for compatibility... > Sat Jan 27 06:58:16 2018: [unset]:_pmi_alps_get_apid:alps response not OKAY Sat Jan 27 06:58:16 2018: [unset]:_pmi_init:_pmi_alps_init returned -1 mmpbsa_py_energy found! Using /opt/apps/intel16/cray_mpich_7_3/amber/16.0/bin/mmpbsa_py_energy > cpptraj found! Using /opt/apps/intel16/cray_mpich_7_3/amber/16.0/bin/cpptraj > Preparing trajectories for simulation... > 5 frames were processed by cpptraj for use in calculation. > Running calculations on normal system... > Beginning GB calculations with /opt/apps/intel16/cray_mpich_7_3/amber/16.0/bin/mmpbsa_py_energy > calculating complex contribution... > calculating receptor contribution... > calculating ligand contribution... > Beginning PB calculations with /opt/apps/intel16/cray_mpich_7_3/amber/16.0/bin/mmpbsa_py_energy > calculating complex contribution... > File "/opt/apps/intel16/cray_mpich_7_3/amber/16.0/bin/MMPBSA.py", line 100, in <module> > app.run_mmpbsa() > File "/opt/apps/intel16/cray_mpich_7_3/amber/16.0/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa > self.calc_list.run(rank, self.stdout) > File "/opt/apps/intel16/cray_mpich_7_3/amber/16.0/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run > calc.run(rank, stdout=stdout, stderr=stderr) > File "/opt/apps/intel16/cray_mpich_7_3/amber/16.0/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 431, in run > self.prmtop) + '\n\t'.join(error_list) + '\n') > CalcError: /opt/apps/intel16/cray_mpich_7_3/amber/16.0/bin/mmpbsa_py_energy failed with prmtop /work/01936/jkmorrow/Skp2/docked557/Skp2_557docked.notail/mmpbsa/2nd.try_DS.and.Babel/com.top! > PB bomb in pb_setgrd(): Allocation aborted Exiting. All files have been retained. > > > sbatch MMPBSA.PBS.BASH script > #!/bin/bash > #SBATCH -N 1 # number of nodes requested > #SBATCH -n 48 # total number of mpi tasks requested > #SBATCH -J mmpbsa.pbs.MPI # job name > #SBATCH -o output.%j # output and error file name (%j expands to jobID) > #SBATCH -p normal # queue (partition) -- normal, development, etc. > #SBATCH -t 24:00:00 # run time (hh:mm:ss) - 1.5 hours > #SBATCH -A P-MDA # project name > > # Slurm email notifications are now working on Lonestar 5 #SBATCH --mail-user=jkmorrow.mdanderson.org > #SBATCH --mail-type=begin # email me when the job starts > #SBATCH --mail-type=end # email me when the job finishes -i $PWD/mmpbsa.in > > module load TACC > module load intel/16.0.1 > module load cray_mpich/7.3.0 > module load amber/16.0 > module load python/2.7.12 > module list > > DIR=/work/01936/jkmorrow/Skp2/docked557/Skp2_557docked.notail/mmpbsa/2nd.try_DS.and.Babel/ > echo "DIR = $DIR" > intop='skp.prmtop' > incrd='skp.inpcrd' > > MMPBSA.py -O -i $PWD/mmpbsa.in -o $PWD/mmpbsa_MPI.out -sp $PWD/com_solvated.top -cp $PWD/com.top -rp $PWD/rec.top -lp $PWD/lig.top -y $PWD/MD4_production.mdcrd > > > John Morrow > Experimental Therapeutics > M.D. Anderson Cancer Center > ________________________________________ > From: Ray Luo [rluo.uci.edu] > Sent: Friday, January 19, 2018 5:57 PM > To: AMBER Mailing List > Subject: Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C > > John, > > Looks like you are using amber14. Please use the latest amber release and the option of radiopt=0 will work. > > 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 19, 2018 at 3:14 PM, Morrow,John Kenneth <JKMorrow.mdanderson.org> wrote: >> I have been receiving the above error when trying to run MMPBSA. I searched the previous posts about this error, and have tried changing setting inp=1 and radiopt=0 in the &pb, but this does not solve the problem. >> >> If I am reading the error correctly, the radius is not set for the 7th atom (CB atom) on the first residue in the structure, and I have tried multiple programs to prepare the protein (MOE, Pymol, Babel), and the atom/atom type does not seem to be atypical. >> >> Input file for running PB and GB in serial: >> &general >> startframe=5, endframe=600, interval=10, keep_files=0, / &gb igb=5, >> saltcon=0.150 / &pb istrng=0.15, fillratio=4.0 / >> >> It returns with the following error: >> >> Running calculations on normal system... >> >> Beginning GB calculations with >> /opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/mmpbsa_py_energy >> calculating complex contribution... >> calculating receptor contribution... >> calculating ligand contribution... >> >> Beginning PB calculations with >> /opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/mmpbsa_py_energy >> calculating complex contribution... >> File "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/MMPBSA.py", line >> 104, in <module> >> app.run_mmpbsa() >> File >> "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packag >> es/MMPBSA_mods/main.py", line 218, in run_mmpbsa >> self.calc_list.run(rank, self.stdout) File >> "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packag >> es/MMPBSA_mods/calculation.py", line 82, in run calc.run(rank, >> stdout=stdout, stderr=stderr) File >> "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packag >> es/MMPBSA_mods/calculation.py", line 431, in run >> self.prmtop) + '\n\t'.join(error_list) + '\n') >> CalcError: /opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/mmpbsa_py_energy failed with prmtop /work/01936/jkmorrow/2nd.try_DS.and.Babel/com.top! >> PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C >> >> Exiting. All files have been retained. >> >> Any other suggestions to resolve this issue would be greatly >> appreciated, thanking you in advance, > The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems. > > > _______________________________________________ > 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 Thu Mar 01 2018 - 17:00:02 PST