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 Fri Oct 30 2015 - 17:30:03 PDT
