Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1

From: Jason Swails <>
Date: Wed, 14 Jan 2015 14:24:22 -0500

On Tue, Jan 13, 2015 at 11:46 PM, Kenneth Huang <
> 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 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 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 had done it.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 14 2015 - 11:30:12 PST
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