George,
Just to check, did you include -O when you're running MMPBSA? If not, it
could lead to some issues.
Otherwise, I've never seen a CalcError and MMPBSA looking like its
completed. Do the contents of _MMPBSA_complex_gb.mdout look alright?
Best,
Kenneth
On Tuesday, May 12, 2015, George Tzotzos <gtzotzos.me.com
<javascript:_e(%7B%7D,'cvml',
'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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Received on Tue May 12 2015 - 07:30:03 PDT
