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

From: Sangita Kachhap <>
Date: Tue, 11 Aug 2015 07:09:01 -0500


I have taken default input just to check of AMBER14, following
are the inputs.

#input file for GB and PB calculation

On 2015-08-11 6:53 am, Jason Swails wrote:

> On Tue, Aug 11, 2015 at 6:05 AM, Sangita Kachhap <>
> wrote:
>> Dear AMBER users I am running for calculation but it is not completing, giving following error. File "/home/amber/amber14/bin/", line 96, in <module> app.run_mmpbsa() File "/home/amber/amber14/bin/MMPBSA_mods/", line 218, in run_mmpbsa, self.stdout) File "/home/amber/amber14/bin/MMPBSA_mods/", line 79, in run, stdout=stdout, stderr=stderr) File "/home/amber/amber14/bin/MMPBSA_mods/", line 416, in run self.prmtop) + 'nt'.join(error_list) + 'n') CalcError: /home/amber/amber14/bin/mmpbsa_py_energy failed with prmtop comp.prmtop! PB Bomb in pb_aaradi(): No radius assigned for atom 17 CB C8 Exiting. All files have been retained.
> ​What is your input file?

Sangita Kachhap
Senior Research Fellow
C/O Dr. Balvinder Singh
Bioinformatics centre
CSIR-Institute of Microbial Technology
Chandigarh, Sector-39A, INDIA
AMBER mailing list
Received on Tue Aug 11 2015 - 05:30:04 PDT
Custom Search