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

From: Ray Luo <>
Date: Fri, 19 Jan 2018 15:57:11 -0800


Looks like you are using amber14. Please use the latest amber release
and the option of radiopt=0 will work.

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
<> 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/", 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/", line 218, in run_mmpbsa
>, self.stdout)
>   File "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packages/MMPBSA_mods/", line 82, in run
>, stdout=stdout, stderr=stderr)
>   File "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packages/MMPBSA_mods/", 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/!
>                 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
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Received on Fri Jan 19 2018 - 16:00:02 PST
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