Jason,
Thanks for the clarification on that regard. MMPBSA.py does still crash at
PB with the same SA Bomb error when scale=1, but I'm going to assume that's
a fault of the lack of available memory.
Best,
Kenneth
On Wed, Jan 14, 2015 at 2:24 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Jan 13, 2015 at 11:46 PM, Kenneth Huang <
> kennethneltharion.gmail.com
> > wrote:
>
> > Ray,
> >
> > It does give an InputError when I try to add in space=1.0 to the py
> script.
> > But setting space=1.0 in the pb.mdin and running mmpbsa_py_energy does
> > complete successfully- the memory usage drops to 18%, while it hovers
> near
> > 54% when space=0.5 in pb.mdin. I'm guessing that the memory usage jumps
> > even more when running MMPBSA.py to the point that it crashes, since I
> was
> > also able to get it to successfully run on another computer with more
> > memory- is the lower memory usage why I'm able to run pb.mdin through
> > mmpbsa_py_energy?
> >
>
> FYI -- The keyword in MMPBSA.py is "scale", not "space". And I believe
> that "space = 1/scale". The default value for 'scale' is 2 (which
> corresponds to a "space" of 0.5).
>
> This was done because that's how mm_pbsa.pl had done it.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Jan 14 2015 - 15:00:03 PST
