Dear Tony,
thanks for your immediate reply.
I copy/paste what I obtain after adding the code line that you suggested:
File "/cluster/scratch/catommas/amber20_src/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/cluster/scratch/catommas/amber20_src/lib/python3.6/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/cluster/scratch/catommas/amber20_src/lib/python3.6/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/cluster/scratch/catommas/amber20_src/lib/python3.6/site-packages/MMPBSA_mods/calculation.py", line 432, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /cluster/scratch/catommas/amber20_src/bin/mmpbsa_py_energy failed with prmtop Complex.prmtop!
As I mentioned, if I use MMPBSA.py everything is fine, although few minutes ago I saw that I obtain the same error when I do a complex stability analysis (that is, when I provide only the prmtop file of the complex).
Thanks again!
Tommaso
________________________________
Da: Tony Yang <tony.tony.tc>
Inviato: martedě 16 giugno 2020 13:23:10
A: AMBER Mailing List
Oggetto: Re: [AMBER] MMPBSA.py error
Hi Tommaso,
It didn’t work as in python still says 'TypeError: a bytes-like object is required, not ‘str’’ or is it a different error now?
Tony
> On 16 Jun 2020, at 12:09, Casalini Tommaso <tommaso.casalini.chem.ethz.ch> wrote:
>
> Dear Tony,
>
> I have the same problem and I have tried to do what you suggested, but it did not work.
>
>
> In this case, I am sure that the input files are correct: the problem arises only with MMPBSA.py.MPI, while the calculation with MMPBSA.py goes well.
>
>
> It seems that the error appears when MMPBSA.py.MPI tries to write the results in the _MMPBSA_complex_pb_mdout.x files.
>
>
> I highlighted such issues some days ago, but I am still waiting for a possible solution.
>
>
> Best regards,
>
> Tommaso
>
> ________________________________
> Da: Tony Yang <tony.tony.tc>
> Inviato: martedě 16 giugno 2020 12:48:25
> A: AMBER Mailing List
> Oggetto: Re: [AMBER] MMPBSA.py error
>
> Hi Tran,
>
> The error is caused by not decoding the error message properly. If you add one line
> out = out.decode("utf-8”)
> after `if calc_failed:` in your calculation.py file under (/Users/lib/python3.6/site-packages/MMPBSA_mods/), likely to be line 429.
>
> Run this again would give you the proper error message output and you can see what was wrong with your calculations.
>
> In terms of the exact error causing the original error report, it was because of a non-standard residue that was not in the optimised radii database. Adding radiopt=0 to the PB namelist fixed our error (see the manual for details regarding radiopt).
>
> Hope this helps :)
>
> Best wishes,
> Tony
>
>> On 15 Jun 2020, at 22:57, Oanh Thuy Ngoc Tran <oanhtt.uci.edu> wrote:
>>
>> Hi,
>> I was wondering if anyone solved this problem on amber archive regarding MMPBSA.py
>>
>> http://archive.ambermd.org/201804/0329.html#start329 <http://archive.ambermd.org/201804/0329.html#start329>
>>
>> I did something similar and I got the same error here
>>
>> ‘
>> File "/Users/lib/python3.6/site-packages/MMPBSA_mods/calculation.py", line 430, in run
>> error_list = [s.strip() for s in out.split('\n')
>> TypeError: a bytes-like object is required, not 'str'
>> Exiting. All files have been retained.
>> ‘
>>
>> Thanks in advance for letting me know.
>>
>> Tran
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Jun 16 2020 - 04:30:05 PDT
