Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C

From: Morrow,John Kenneth <JKMorrow.mdanderson.org> Date: Sat, 27 Jan 2018 14:03:46 +0000

--
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,
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