Two things to try:
set debug_printlevel=2 in your &general section (to print out line numbers
with your error messages
try AmberTools 12 instead of AmberTools 1.5, the script has been improved.
Your error message does not contain enough information for me to debug your
issue (in fact, I can't even say for certain that the issue is due to Amber
or faulty hardware). Also, what happens if you use fewer processors and
fewer frames?
If you get errors in parallel, it is always a good idea to simplify your
calculation to try and narrow down the errors you're seeing (for instance,
in this case use 1 processor with only 2 or 3 frames or something, rather
than 200 frames via 28 cores).
HTH,
Jason
On Mon, Oct 15, 2012 at 2:23 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com>wrote:
> Dear Amber users
>
> I am trying to calculate the decomposition energy for ras-raf complex
> implemented in Tutorial A3, GBSA works and but the PBSA does not work with
> the following error:
>
> Progress.log:
> Running MMPBSA.MPI on 28 processors...
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /share/apps/amber11/bin/ptraj
> sander found! Using /share/apps/amber11/bin/sander for GB calculations
> sander found! Using /share/apps/amber11/bin/sander for PB calculations
> Preparing trajectories for simulation...
> 200 frames were read in and processed by ptraj for use in calculation.
>
> Beginning GB calculations with sander...
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with sander...
> calculating complex contribution...
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> close failed in file object destructor:
> IOError: [Errno 9] Bad file descriptor
> calculating receptor contribution...
> calculating ligand contribution...
>
>
> Your help in this regard would be highly appreciated.
>
> Cheers
> Maryam
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 15 2012 - 05:00:02 PDT
