On Fri, Aug 30, 2013 at 11:30 AM, <psu4.uic.edu> wrote:
> Hello all,
>
> Thanks Jan-Philip's solution. It works! So it seems like our
> trouble-shooting was in the wrong direction : /
>
> However, there is a new error message pops out:
>
> Loading and checking parameter files for compatibility...
> Loading and checking parameter files for compatibility...
> Traceback (most recent call last):
> File "./python_API_2.py", line 21, in <module>
> total_mut = data.mutant['gb']['complex']['TOTAL'].copy()
> *AttributeError: 'mmpbsa_data' object has no attribute 'mutant'*
>
This example was meant primarily to demonstrate a potential use of the API.
Attributes and data keys are created only as they're needed. Therefore,
mmpbsa_data will not have a "mutant" attribute unless you actually run
alanine scanning (thereby generating 'mutant' data).
As general advice with examples of this sort -- analyze the code in the
example so that you understand what each line is doing (this sample script
just computes and plots the autocorrelation function of the total complex
energies -- not likely of much use for what you want to do). It would be
good to cross-reference properties of the 'data' object with how the
AmberTools 13 manual describes the mmpbsa_data data structure. It also
never hurts to be comfortable with using the programming language used in
the example. FWIW, I'm hardly alone in thinking that Python programming is
potentially the most useful
A 'quick fix' for this error of course is to delete all references to the
mutant data. However, while that will give you the satisfaction of
watching the script finish and a graph appear, it is unlikely to provide
you with useful data.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 30 2013 - 10:30:02 PDT
