On Fri, 2015-05-29 at 11:46 +0100, D.J. Pattinson wrote:
> Dear Amber users
>
> I would like to be using the MMPBSA.py API in my work.
>
> I’ve run MMPBSA.py on a pretty standard ligand protein system and
> attempt to then load the the mmpbsa info as described on p637 of the
> Amber 2015 reference manual:
>
> from MMPBSA_mods import API as MMPBSA_API
> data = MMPBSA_API.load_mmpbsa_info(’_MMPBSA_info’)
>
> I get:
>
> AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber'
It seems that I introduced this error when I stopped parsing topology
files as part of the API (which I did to make the API parse the output
almost instantaneously rather than potentially taking several seconds
each time). But it seems that "using_chamber" is only set when topology
files are parsed.
The solution is fairly simple -- edit the _MMPBSA_info file and add the
following line somewhere before the input file is printed:
using_chamber = False
If you're using CHARMM prmtop files, that will need to be set to True.
I'm preparing a fix in which this variable will be printed to the MMPBSA
info file in the future, and I've added a test for the API to make sure
it doesn't break again.
Thanks for the report!
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 29 2015 - 06:30:03 PDT
