Re: [AMBER] error

From: Casalini Tommaso <>
Date: Tue, 16 Jun 2020 11:09:30 +0000

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, while the calculation with goes well.

It seems that the error appears when 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,


Da: Tony Yang <>
Inviato: martedě 16 giugno 2020 12:48:25
A: AMBER Mailing List
Oggetto: Re: [AMBER] 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 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,

> On 15 Jun 2020, at 22:57, Oanh Thuy Ngoc Tran <> wrote:
> Hi,
> I was wondering if anyone solved this problem on amber archive regarding
> <>
> I did something similar and I got the same error here
> ‘
> File "/Users/lib/python3.6/site-packages/MMPBSA_mods/", 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

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Received on Tue Jun 16 2020 - 04:30:03 PDT
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