Thanks so much, Prof.
I am trying it again.
Nadaafiva
On Thu, Oct 30, 2014 at 12:44 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Oct 28, 2014 at 10:38 PM, asdda asa <nadaafiva.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I am performing entropy calculation using nmode.
> >
> > My system consist of a protein with 213 residue and a ligand.
> >
> > First, I did a try with only 4 frames and drms=0.1.
> >
> > My calculation succeed to reach convergence, but then fail with
> following
> > message:
> >
> > Line minimizer aborted: step at upper bound 0.061508653
> >
> > Line minimizer aborted: step at upper bound 0.011450028
> >
> > Line minimizer aborted: step at upper bound 0.025196144
> >
> > Line minimizer aborted: step at upper bound 0.044987034
> >
> > Line minimizer aborted: step at upper bound 0.00036005744
> >
> > Line minimizer aborted: step at upper bound 0.003992881
> >
> > FATAL: allocation failure in vector()
> >
> > CalcError: /usr/local/AMBER/amber12/bin/mmpbsa_py_nabnmode failed with
> > prmtop complex.prmtop!
> >
> > Exiting. All files have been retained.\
> >
> >
> > From the massage, the problem might be due to prmtop file,
> >
>
> No, the error message was simply telling you where the calculation died
> (not why it died). It's possible that the prmtop file has problems that
> make finding a minimum difficult, but I doubt that is the case.
>
> The actual problem is the "allocation failure", which indicates that a
> malloc call failed. As far as I know, memory allocation fails either when
> there is not enough memory available or when some memory becomes corrupt
> (due to a bug in the program).
>
>
> > but I was using the same prmtop file to calculate entalphy, and it was
> >
> > succesfull.
> >
> >
> > I am using a single computer with 48 GB memory, so it should be no
> problem
> >
>
> That does make the error more puzzling. However, it is not always the
> case that a program has access to all of the physical memory in the system
> (a 32-bit program, for instance, cannot address more than ~4GB of memory).
> Also, depending on how large your system is, it is still possible that 48
> GB is not enough. The Hessian matrix is 3N x 3N (since it's symmetric, the
> actual requirement is a little more than half that number). At full double
> precision (8 bytes per number), 48 GB would be consumed completely by
> ~20-30 thousand atoms (assuming the full Hessian is stored rather than just
> the upper- or lower-triangular portion). While this is very big for an
> unsolvated system, it is not unfathomably large.
>
> If you still can't get this working, we would need to be able to reproduce
> the problem on our own machine(s) to help further.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Oct 29 2014 - 21:00:02 PDT
