Hi Tony,
I think it works. Thank you so much for your help.
Tran
On Tue, Jun 16, 2020 at 3:49 AM Tony Yang <tony.tony.tc> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Oanh Tran *
Poulos Lab
graduate student
Department of Chemistry
*University of California at Irvine*
oanhtt.uci.edu <Otran1213.gmail.com>
832-571-5504
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 17 2020 - 14:30:03 PDT
