Hi Tommaso,
I’ve never encountered this error before. I believe internally MMPBSA.py.MPI is the same as MMPBSA.py and they both use the same mmpbsa_py_energy program for MMPBSA energy computation. I don’t see any reason one would say prmtop error and the other doesn’t? I can’t offer much suggestion other than maybe run ante-MMPBSA.py to generate the topology files again. Or you can run the mmpbsa_py_energy program directly to compare?
Sorry I’m not much help here.
Tony
> On 16 Jun 2020, at 12:28, Casalini Tommaso <tommaso.casalini.chem.ethz.ch> wrote:
>
> 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: martedì 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: martedì 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 - 05:00:02 PDT
