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 - 07:30:02 PDT
