Hi,
Thanks for the reply. Is there some way to do minimization in SANDER using
a trajectory file as an input??
Thanks.
On Thu, Sep 18, 2014 at 5:07 PM, Jason Swails <jason.swails.gmail.com>
wrote:
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> 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 - 07:30:04 PDT
