Re: [AMBER] Error in unit 9 inpcrd file

From: KIRTANA S <skirtana4.gmail.com>
Date: Sun, 17 Jul 2011 22:36:23 -0400

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
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> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Sun Jul 17 2011 - 20:00:03 PDT
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