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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Received on Wed Mar 22 2017 - 08:30:03 PDT
