I have taken default input just to check MMPBSA.py of AMBER14, following
are the inputs.
#input file for GB and PB calculation
&general
startframe=5
endframe=100
interval=5,
verbose=2
keep_files=0
/
&gb
igb=5,
saltcon=0.150,
/
&pb
istrng=0.15
fillratio=4.0
/
On 2015-08-11 6:53 am, Jason Swails wrote:
> On Tue, Aug 11, 2015 at 6:05 AM, Sangita Kachhap <sangita.imtech.res.in>
> wrote:
>
>> 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> app.run_mmpbsa() File "/home/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/home/amber/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/home/amber/amber14/bin/MMPBSA_mods/calculation.py", 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
----------------------------------------------
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Received on Tue Aug 11 2015 - 05:30:04 PDT
