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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 Wed, Apr 11, 2018 at 7:47 AM, Kasprzak, Wojciech (NIH/NCI) [C] <wojciech.kasprzak.nih.gov> wrote: > Dear Amber Users, > > This is Voytek Kasprzak from Frederick National Lab (NCI). I am unable to complete a simple > MMPBSA run based on Amber Advanced Tutorial 3 (section 3.4) in Amber 16 or Amber 14. > My case is similar but not the same as a post on the PB failure from yesterday. > > I am analyzing a trajectory of an RNA fragment with a small ligand (~60 atoms), that was > subjected to explicit solvent PME MD simulation in Amber 16. All topology files > (complex in solvent, complex without solvent, receptor alone and ligand alone) were created > in one LEaP session with the same PBRadii - a potential issue, as the end of the FILE.o* > shown below seems to suggest (see 1. below) > > After completing successfully the GB-based section of the MMPBSA.py.MPI run (10,000 input > frames on 16 cores), the program crashes reproducibly as it gets to the PB-based calculations. > The error message states that "No radius assigned for atom 3 C5' CI" is the problem, > and one PB output file _MMPBSA_complex_pb.mdout.2 shows an aborted start of that section > (see 2. below). C5' is the third atom in the RNA/lifand prmtop file (oddly, no complaints > about the first two atoms: HO5' and O5'). The input file is shown in point 3. > > Should I create separate no-solvent topology files with PBRadii set to bondi since that is > the common denominator for igb=2 and pbsa runs? What would you recommend for RNA/DNA-ligand > complexes? What are the consequences of having solvent run based on one set of radii and > solvent-free parts on another? > If my interpretation of the error messages is incorrect, what else could be the problem? > > Best regards, Voytek > > Wojciech (Voytek) Kasprzak (Contractor) > Analyst Programmer > Frederick National Laboratory for Cancer Research > Leidos Biomedical Research, Inc. > Post Office Box B > Frederick, Maryland 21702 > Phone: 301-846-5537 > kasprzaw.mail.nih.gov > http://binkley2.ncifcrf.gov/users/kasprzak > > ================================================================== > 1. Error message: > > File "/opt/nasapps/production/amber/amber16/bin/MMPBSA.py.MPI", line 100, in <module> > app.run_mmpbsa() > File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa > self.calc_list.run(rank, self.stdout) > File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run > calc.run(rank, stdout=stdout, stderr=stderr) > File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run > self.prmtop) + '\n\t'.join(error_list) + '\n') > CalcError: /opt/nasapps/production/amber/amber16/bin/mmpbsa_py_energy failed with prmtop RNA-LIGAND-nosolv.prmtop! > PB Bomb in pb_aaradi(): No radius assigned for atom 3 C5' CI > > Error occured on rank 2. > Exiting. All files have been retained. > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD > with errorcode 1. > ================================================================== > 2. Last PB output before the crash (_MMPBSA_complex_pb.mdout.2): > Reading parm file (RNA-LIGAND-nosolv.prmtop) > title: > default_name > mm_options: e_debug=3 > mm_options: ipb=2 > mm_options: inp=2 > mm_options: epsin=1.000000 > mm_options: epsout=80.000000 > mm_options: smoothopt=1 > mm_options: istrng=150.000000 > mm_options: radiopt=1 > mm_options: dprob=1.400000 > mm_options: iprob=2.000000 > mm_options: npbopt=0 > mm_options: solvopt=1 > mm_options: accept=0.001000 > mm_options: maxitn=1000 > mm_options: fillratio=4.000000 > mm_options: space=0.500000 > mm_options: nfocus=2 > mm_options: fscale=8 > mm_options: bcopt=5 > mm_options: eneopt=2 > mm_options: cutnb=0.000000 > mm_options: sprob=0.557000 > mm_options: cavity_surften=0.037800 > mm_options: cavity_offset=-0.569200 > Processing ASCII trajectory (_MMPBSA_complex.mdcrd.2) > > Processing frame 1 > iter Total bad vdW elect nonpolar EPB frms > eff.c(2717) enb14 --> 571.724 > eff.c(2718) eel14 --> -6929.892 > ================================================================== > 3. MMPBSA input file (same as in the tutorial) mmpbsa.in: > Input file for running PB and GB (100ns in 10K frames) > &general > endframe=10000, verbose=1, > # entropy=1, > / > &gb > igb=2, saltcon=0.15 > / > &pb > istrng=0.15, > / > ================================================================== > > > _______________________________________________ > 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 Wed Apr 11 2018 - 10:00:03 PDT