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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 12:47 PM, Kasprzak, Wojciech (NIH/NCI) [C] <wojciech.kasprzak.nih.gov> wrote: > Dr. Luo, > > Thank you very much! Indeed, I now have a run under way with radiopt=0. > > I would still like to understand if there are any potential problems with using > PME-based trajectory with, say mbondi2 or mbondi parameters in the topology file > with a follow-up MMPBSA PB calculations for which the Amber manual > recommends bondi parameters. > > Also, in principle, if I have a trajectory based on explicit solvent run, but with only > the RNA & ligand atoms saved, will the MMPBSA calculation run with the solvent-free > topology file used twice for the -sp and -cp parameters? > > Thank you again, and I would appreciate some clarification of the remaining > two questions. > > 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 > > ________________________________________ > From: Ray Luo [rluo.uci.edu] > Sent: Wednesday, April 11, 2018 12:46 PM > To: AMBER Mailing List > Subject: Re: [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex > > Voytek, > > Set radiopt=0 to use the radii in the prmtop file should resolve this issue. > > 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 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. > >> >> >> _______________________________________________ >> 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 Wed Apr 11 2018 - 19:00:02 PDT