[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Tue, 11 Aug 2015 05:05:20 -0500


Dear AMBER users

I am running MMPBSA.py for calculation but it is not completing, giving
following error.

File "/home/amber/amber14/bin/MMPBSA.py", line 96, in <module>
 File "/home/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in
 self.calc_list.run(rank, self.stdout)
 File "/home/amber/amber14/bin/MMPBSA_mods/calculation.py", line 79, in
 calc.run(rank, stdout=stdout, stderr=stderr)
 File "/home/amber/amber14/bin/MMPBSA_mods/calculation.py", line 416, in
 self.prmtop) + 'nt'.join(error_list) + 'n')
CalcError: /home/amber/amber14/bin/mmpbsa_py_energy failed with prmtop
 PB Bomb in pb_aaradi(): No radius assigned for atom 17 CB C8

Exiting. All files have been retained.

Is this error associate with any compilation problem? Version of python
on my system is 2.6.6

Sangita Kachhap
Senior Research Fellow
C/O Dr. Balvinder Singh
Bioinformatics centre
CSIR-Institute of Microbial Technology
Chandigarh, Sector-39A, INDIA
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Received on Tue Aug 11 2015 - 03:30:03 PDT
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