Hi,
Thanks.
From your explanations, I guess that my problem was that I was using
the MMPBSA API from AmberTools15 to read data obtained with MMPBSA.py
from AmberTools13. I'm going to make sure that I use the same version
for both generating the _MMPBSA_info file and for its analysis.
Thanks again,
Gerald.
On 06/23/2015 04:32 PM, Jason Swails wrote:
> On Tue, Jun 23, 2015 at 9:49 AM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
>> Hello,
>>
>> In the same spirit as an earlier email. I'm trying to load MMPBSA.py
>> results with the MMPBA API.
>> My scripts, in the spirit of the Amber documentation (section 31.4),
>> starts with:
>> import os
>> import sys
>> sys.path.append(os.path.join(os.getenv('AMBERHOME'), 'bin'))
>>
>
> This line is no longer necessary for AmberTools 15 (since amber.sh
> automatically puts these modules in PYTHONPATH).
>
>
>
>> from MMPBSA_mods import API as MMPBSA_API
>> results = MMPBSA_API.load_mmpbsa_info('_MMPBSA_info')
>>
>> In AmberTools13, no problem:
>> >>> results = MMPBSA_API.load_mmpbsa_info('_MMPBSA_info')
>> Loading and checking parameter files for compatibility...
>>
>> In AmberTools15:
>> >>> results = MMPBSA_API.load_mmpbsa_info('_MMPBSA_info')
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in <module>
>> File
>> "/opt/amber15-gnu/lib/python2.6/site-packages/MMPBSA_mods/API.py", line
>> 358, in load_mmpbsa_info
>> app.parse_output_files()
>> File
>> "/opt/amber15-gnu/lib/python2.6/site-packages/MMPBSA_mods/main.py", line
>> 928, in parse_output_files
>> self.using_chamber)}
>> AttributeError: 'MMPBSA_App' object has no attribute 'using_chamber'
>>
>
> Indeed, this issue was raised recently, and I issued a fix in update.1 for
> AmberTools 15. The quick workaround for the time being is to add the line
>
> using_chamber = False
>
> somewhere in the _MMPBSA_info file (but not in the text of the input file
> at the very end). Note that update.1 fixes the *creation* of _MMPBSA_info
> to make sure this attribute is properly added, so update.1 won't make a
> _MMPBSA_info file generated with an unpatched MMPBSA.py start working. You
> need to actually add that variable. (As another note, obviously change
> False to True if your prmtop files are chamber-style prmtops implementing
> the CHARMM force field).
>
>
>> I have checked the source code and could not see any definition of
>> using_chamber in the python parts.
>> Any idea?
>>
>
> using_chamber was assigned when the prmtop files were parsed. AmberTools
> 13 parsed the prmtop files as part of the MMPBSA.py API, so this attribute
> was properly set. However, none of the prmtop information is actually
> *used* in the API, so it just slowed down the API significantly. Which is
> why prmtop files *stopped* getting read in AmberTools 15 (the data is
> populated almost immediately now rather than requiring up to tens of
> seconds to parse).
>
> All the best,
> Jason
>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
____________________________________________________________________________
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 23 2015 - 08:00:04 PDT
