hello
issue is with our .inpcr file
the coordinates have got merged
5.76869501001.4057050 -3.7700960 6.11179501000.4336050 -3.3678960
6.28819501002.2123050 -3.2505960 4.68249501001.5071050 -3.6185960
8.37599501002.1275050 -4.7962960 7.95059501000.0834050 -4.7291960
9.45079501007.9152050 -5.1452960 9.68089501007.0689050 -4.4926960
i might not be correct but you edit the file such that column number are
proper maintained for e.g
5.76869*50*1001.4057050 -3.7700960 6.11179*50*1000.4336050 -3.3678960
5.76869 1001.4057050 -3.7700960 6.11179 1000.4336050 -3.3678960
somebody else can guide better on this but the issue is due to merger of
coordinates.
On Mon, Jul 18, 2011 at 8:06 AM, KIRTANA S <skirtana4.gmail.com> wrote:
> Below are some details :
> Error message:
>
> forrtl: severe (64): input conversion error, unit 9, file
> /kr/pmma/md/pmma_500mer.inpcrd
> Image PC Routine Line Source
>
> sander.MPI 0000000000A3F8CA Unknown Unknown Unknown
> sander.MPI 0000000000A3E85C Unknown Unknown Unknown
> sander.MPI 00000000009F312E Unknown Unknown Unknown
> sander.MPI 00000000009A227B Unknown Unknown Unknown
> sander.MPI 00000000009A1B68 Unknown Unknown Unknown
> sander.MPI 00000000009C36C2 Unknown Unknown Unknown
> sander.MPI 000000000050238C Unknown Unknown Unknown
> sander.MPI 00000000004BA0EF Unknown Unknown Unknown
> sander.MPI 00000000004B893E Unknown Unknown Unknown
> sander.MPI 0000000000405E42 Unknown Unknown Unknown
> libc.so.6 0000003060A1D994 Unknown Unknown Unknown
> sander.MPI 0000000000405D69 Unknown Unknown Unknown
> Fatal error in PMPI_Bcast: Other MPI error, error stack:
> PMPI_Bcast(1302)..................: MPI_Bcast(buf=0x156ae20, count=154,
> MPI_INTE
> GER, root=0, MPI_COMM_WORLD) failed
> MPIR_Bcast(1031)..................:
> MPIR_Bcast_binomial(157)..........:
> MPIC_Recv(83).....................:
> MPIC_Wait(519)....................:
>
>
> Protocol I am using to run amber :
> mpiexec_hydra $AMBERHOME/exe/sander.MPI -O -i min.in -o min.out -p
> pmma_500mer.
> prmtop -c pmma_500mer.inpcrd -ref pmma_500mer.inpcrd -r min.restrt
>
> min.in
>
> minimization
> &cntrl
> imin=1, ntx=1, drms=0.01,
>
> irest=0, ntxo=1, cut=15.0,
>
> ntpr=100, ntwx=100, ntwe=100,
>
> maxcyc=10000, ncyc=1000,
> igb=6,ntt=0,
> ntb=0,
> &end
>
> I have attached the inpcrd file. If required I can send the initial file.
>
> Thanks
> kirtana
>
> On Sun, Jul 17, 2011 at 9:40 PM, case <case.biomaps.rutgers.edu> wrote:
> > On Sun, Jul 17, 2011, KIRTANA S wrote:
> >>
> >> I am using a polymer chain of 500 repeating units, the same works for
> >> 200mer long chain.
> >> The 500mer fails for the minimization run with the error in unit 9
> inpcrd file .
> >
> > Can you cut and paste the *exact* error message? And, give the command
> line
> > you are using to run amber (again, make every effort to be completely
> > accurate.)
> >
> > ...thanks...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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>
>
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Received on Mon Jul 18 2011 - 02:30:02 PDT
