AMBER Archive (2003)

Subject: Re: run sander?

From: quch quch (quch0_at_yahoo.com)
Date: Mon Jun 02 2003 - 13:52:22 CDT

Dear Prof. Case,
Thanks for you reply. They are actually in amber6 not
amber7 on single sgi machine. Is there any mistake in
the input file?
Thanks,
quchen

--- "David A. Case" <case_at_scripps.edu> wrote:
> On Mon, Jun 02, 2003, quch quch wrote:
>
> > I have problem to run sander on test file, could
> > anyone tell me what is wrong with the input file?
> >
> > Input file ($AMBERHOME/test/vac_rna):
> >
> > mpirun -np 1 sander -O -i gbin -c md4.x -o
> test.out
> >
> > Output has errors like this:
> > =============================
> > 1. RESOURCE USE:
> >
> >
> > EWALD SPECIFIC INPUT:
> >
> > | Using the SGI specific (ZFFT3D) Fast Fourier
> > Transform
> > | Using the T3D specific (FFT3D0) Fast Fourier
> > Transform
> > Largest sphere to fit in unit cell has radius
> =
> > 0.000
> >
> > Ewald PARAMETER RANGE CHECKING:
> > parameter skinnb+cutoffnb: (nonbond list cut)
> has
> > value 0.10000E+03
> > This is outside the legal range
> > Lower limit: 0.00000E+00 Upper limit:
> 0.00000E+00
> > Check ew_legal.h
> > ============================
> >
>
> This is weird. You can look at the sample output,
> mdout.min.save, and compare
> it to yours. It should not have anything like
> "EWALD SPECIFIC INPUT" in
> the output, and having it say that you are using
> both SGI and T3D FFT's
> seems odd.
>
> What machine are you running on? Which MACHINE file
> did you use? If you
> can't figure anything out, please post the complete
> output file.
>
> Is there any chance that the "sander" in your path
> is actually amber6 sander
> rather than amber7 sander? (Type "which sander" to
> see what you are getting.)
>
> ..regards...dac
>
> --
>
>
==================================================================
> David A. Case | e-mail:
> case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax:
> +1-858-784-8896
> The Scripps Research Institute | phone:
> +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
>
> La Jolla CA 92037 USA |
> http://www.scripps.edu/case
>
==================================================================
>

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