You will need Python 2.6 or higher to use MMPBSA.py and MMPBSA.py.MPI. The
'format' command in python was implemented in Python 2.6. Thus, you will
have to upgrade your python version before this command will work.
Good luck!
-Bill
On Mon, Sep 27, 2010 at 1:05 PM, Anuradha Mittal
<anuradha.mittal.gmail.com>wrote:
> Hi,
>
> I get the following error when I run the MMPBSA.py.MPI
>
> Traceback (most recent call last):
> File "/u/ac/amitta2/amber11/bin/MMPBSA.py.MPI", line 380, in <module>
> print >> sys.stdout, 'MMPBSA.py.MPI being run on {0}
> processors'.format(mpi_size)
> AttributeError: 'str' object has no attribute 'format'
>
>
> The job script looks like this:
> #!/bin/tcsh
> #PBS -l walltime=00:30:00
> #PBS -q normal
> # Run on 64 cores
> #PBS -l nodes=1:ppn=3
> #PBS -V
> #PBS -N testjob
> #PBS -A TG-MCB090168
>
> mvapich2-start-mpd
> setenv NP `wc -l ${PBS_NODEFILE} | cut -d'/' -f1`
> setenv PYTHONPATH /u/ac/amitta2/lib/python/
> setenv AMBERHOME ~/amber11
> setenv MV2_SRQ_SIZE 4000
> cd /cfs/scratch/users/amitta2/fabh
> mpirun -machinefile ${PBS_NODEFILE} -np ${NP} $AMBERHOME/bin/MMPBSA.py.MPI
> -O -i mmpbsa_per_res_decomp.in -o final_results_mmpbsa.dat -sp
> com_solvated.top -cp com.top -rp rec.top -lp lig.top -y md13.x
> mpdallexit
>
>
>
> When I compiled mmpbsa.py.mpi I got the following:
>
> /bin/bash setup.sh
> Python version 2 detected. No file conversion necessary.
> 'import site' failed; use -v for traceback
> /bin/cp MMPBSA.py.MPI *pyc /u/ac/amitta2/amber11/bin
>
>
> I have Python-2.5.2 and mvapich2-1.2-intel-ofed-1.2.5.5.
>
> Thanks
> Anu
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Sep 27 2010 - 11:00:10 PDT
