Thank you Jason,
I was running mmpbsa.py but inadvertently I used the following script:
mpirun -np 12 MMPBSA.py -O -i decomp.in -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP__MMPBSA.dat -sp complex_solv.prmtop -cp subA-subB.prmtop -rp subA.prmtop -lp subB.prmtop -y 10frame.nc
The culprit seems to be the ‘mpirun -np 12’. Skipping this produces no error.
On 12 May 2015, at 19:03, Jason Swails <jason.swails.gmail.com> wrote:
> Could you be trying to run in parallel? If so, are you using
> MMPBSA.py.MPI, or are you using MMPBSA.py?
>
> On Tue, May 12, 2015 at 10:15 AM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Following yesterday’s message thread ("mmpbsa.py error”), I run mmpbsa.py
>> according to Jason’s suggestion. The program seems to run fine, producing
>> output files as expected as well as the stats of the run. Here’s the output.
>>
>> I’m not sure how significant is the CalcError message. Is it a matter of
>> concern or is it a bug?
>>
>> MMPBSA.py Finished! Thank you for using. Please cite us if you publish
>> this work with this paper:
>> Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke,
>> H. and Roitberg, A. E.
>> J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321
>> sander found! Using /Users/gtzotzos/Programs/MD/amber12/bin/sander
>> cpptraj found! Using /Users/gtzotzos/Programs/MD/amber12/bin/cpptraj
>>
>> Timing:
>> Total setup time: 0.051 min.
>> Creating trajectories with cpptraj: 0.091 min.
>> Total calculation time: 2.121 min.
>>
>> Total GB calculation time: 2.121 min.
>>
>> Statistics calculation & output writing: 0.006 min.
>> Total time taken: 2.269 min.
>>
>>
>> MMPBSA.py Finished! Thank you for using. Please cite us if you publish
>> this work with this paper:
>> Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke,
>> H. and Roitberg, A. E.
>> J. Chem. Theory Comput., 2012, 8 (9) pp 3314--3321
>> sander found! Using /Users/gtzotzos/Programs/MD/amber12/bin/sander
>> cpptraj found! Using /Users/gtzotzos/Programs/MD/amber12/bin/cpptraj
>>
>> Error opening unit 16: File "_MMPBSA_restrt.0" exists (use -O to
>> overwrite)
>> CalcError: /Users/gtzotzos/Programs/MD/amber12/bin/sander failed with
>> prmtop subB.prmtop!
>> Exiting. All files have been retained.
>> sander found! Using /Users/gtzotzos/Programs/MD/amber12/bin/sander
>> cpptraj found! Using /Users/gtzotzos/Programs/MD/amber12/bin/cpptraj
>>
>>
>> ===================================================================================
>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>> = EXIT CODE: 1
>> = CLEANING UP REMAINING PROCESSES
>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>
>> ===================================================================================
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>>
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue May 12 2015 - 11:00:02 PDT
