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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 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-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/14.0/lib/python2.6/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/14.0/lib/python2.6/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/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, > > John > 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 Fri Jan 19 2018 - 16:00:02 PST