Re: [AMBER] Error message

From: David A Case <>
Date: Thu, 29 Jul 2021 13:55:29 -0400

On Wed, Jul 28, 2021, Vento, Gabby wrote:
>I am attempting to run some simulations. However, the simulation will not
>complete due to the error message I keep receiving. Could someone please
>tell me what this error message means and how I can fix it?
> File "/N/soft/rhel7/amber/gpu/intel/18/amber18/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'

This is an python2 vs python3 problem. When AmberTools18 was released, it
was restricted to python2, but you are using python3. Two options:

1. in $AMBERHOME, run ./update_amber --upgrade This will upgrade you
to AmberTools19, which should be compatible with python3.

2. Download AmberTools21, and install in its own folder. Use that for
everything related to AmberTools, and just use Amber18 for pmemd. This gets
you many more fixes and updates that just going to AmberTools19.

...good luck....dac

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Received on Thu Jul 29 2021 - 11:00:02 PDT
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