Hi,
In addition to what Prof. Case stated, I added a check to
mmpbsa_entropy.nab that checks the convergence after the minimization. So
as long as you do not see
----Not minimized properly!----
---- Entropy not Calculated----
in the output file then you should be okay and what you see is probably
just a warning.
Best,
Dwight
On Wed, Mar 22, 2017 at 11:12 AM, David Case <david.case.rutgers.edu> wrote:
> On Tue, Mar 21, 2017, konda003 . wrote:
> >
> > I am running entropy for protein-ligand complex using NMODE. I got the
> > deltaS result, but it shows the below message while running the job. I
> get
> > the same message, even i try with single frame or many frames. Is the
> > result acceptable? I have seen the previous amberlist responses, they
> said
> > that minimization is getting stuck. How to overcome this? Do we need to
> run
> > many minimization steps before running MD?
> >
> > Line minimizer aborted: step at upper bound 0.0020765772
> > Line minimizer aborted: step at upper bound 0.0018317604
> > Line minimizer aborted: step at upper bound 0.0015270612
> > Line minimizer aborted: step at upper bound 0.047828871
> > Line minimizer aborted: step at upper bound 0.030144341
> > Line minimizer aborted: step at upper bound 0.12217309
>
> Check the output files to see whether the calculation eventually got to an
> accurate minimum or not. Find a single frame where you get this problem,
> and try the nmode calculation "by hand", looking at the output carefully.
> If this only happens for one particular frame, you can probably skip that
> one.
>
> Others on the list probably know more about this than I do. It's not even
> clear to me whether the above is just a warning or not.
>
> ....dac
>
>
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>
--
T. Dwight McGee Jr.
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Wed Mar 22 2017 - 09:30:04 PDT
