On Thu, 2014-09-18 at 13:30 +0530, Sourav Purohit wrote:
> While peforming entropy calculation using MMPBSA.py, I get the message:
>
> Line minimizer aborted: step at upper bound 0.074487672
> Line minimizer aborted: step at upper bound 0.00086134154
> Line minimizer aborted: step at upper bound 0.0014747638
> Line minimizer aborted: step at upper bound 0.012288468
> Line minimizer aborted: step at upper bound 0.055832154
> Line minimizer aborted: step at upper bound 0.00056890766
> Line minimizer aborted: step at upper bound 7.3399234e-05
> Line minimizer aborted: step at upper bound 0.096555206
> Line minimizer aborted: step at upper bound 0.0012406
>
> and this continues.
> What should be done to get rid of this??
This indicates that the minimizer is having a hard time finding a local
minimum. There's not much you can do about it short of finding another
way to minimize your structures before feeding it to MMPBSA.py. If a
minimum cannot be found, that snapshot will likely be skipped when doing
the normal mode calculations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 18 2014 - 05:00:03 PDT
