Hi Jason,
It’s already set to this by default (I think), but I added it explicitly. I still get the same error.
Here’s is my mmpbsa input file:
&general
verbose=1,
entropy=1,
/
&pb
istrng=0.150,
radiopt=1,
/
&nmode
nmode_istrng=0.150,
> On Oct 30, 2015, at 6:18 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> Just set radiopt=1 in the &pb section.
>
> HTH,
> Jason
>
> --
> 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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Received on Sat Oct 31 2015 - 10:30:05 PDT
