Re: [AMBER] mmpbsa.py error

From: Jason Swails <jason.swails.gmail.com> Date: Fri, 30 Oct 2015 20:18:33 -0400

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
> On Oct 30, 2015, at 8:08 PM, Mohammad Salem <mohammad.alaraby.gmail.com> wrote:
> 
> Hi All,
> 
> I am receiving this error and I checked the previous helps by Jason on it (thanks, Jason!)
> 
>    PB Bomb in pb_aaradi(): No radius assigned for atom     7  CB    C8
> 
> I tried to edit all the C8 atom types to C; that’s the output from a second parmed run:
> 
> change AMBER_ATOM_TYPE: Nothing to do
> ParmWarning: change AMBER_ATOM_TYPE: @%C8 matches no atoms
> Done!
> 
> Now, still, I get the same error:
> 
> 
>  calculating complex contribution...
>  File "/Applications/amber14/bin/MMPBSA.py", line 104, in <module>
>    app.run_mmpbsa()
>  File "/Applications/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
>    self.calc_list.run(rank, self.stdout)
>  File "/Applications/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
>    calc.run(rank, stdout=stdout, stderr=stderr)
>  File "/Applications/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 431, in run
>    self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /Applications/amber14/bin/mmpbsa_py_energy failed with prmtop complex.top!
>    PB Bomb in pb_aaradi(): No radius assigned for atom     7  CB    C8
> 
> What am I doing wrong?
> 
> Thanks!
> 
> Mohammad
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