ptraj found! Using /net/bccs/cbu/linux64/amber11/bin/ptraj sander found! Using /net/bccs/cbu/linux64/amber11/bin/sander ptraj found! Using /net/bccs/cbu/linux64/amber11/bin/ptraj ptraj found! Using /net/bccs/cbu/linux64/amber11/bin/ptraj sander found! Using /net/bccs/cbu/linux64/amber11/bin/sander sander found! Using /net/bccs/cbu/linux64/amber11/bin/sander ptraj found! Using /net/bccs/cbu/linux64/amber11/bin/ptraj sander found! Using /net/bccs/cbu/linux64/amber11/bin/sander ptraj found! Using /net/bccs/cbu/linux64/amber11/bin/ptraj sander found! Using /net/bccs/cbu/linux64/amber11/bin/sander ptraj found! Using /net/bccs/cbu/linux64/amber11/bin/ptraj sander found! Using /net/bccs/cbu/linux64/amber11/bin/sander Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi) Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi) Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi) Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi) Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi) Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi) Preparing trajectories with ptraj... Preparing trajectories with ptraj... Preparing trajectories with ptraj... Preparing trajectories with ptraj... Preparing trajectories with ptraj... Preparing trajectories with ptraj... mpirun: killing job... -------------------------------------------------------------------------- mpirun noticed that process rank 0 with PID 6058 on node korgpil.bccs.uib.no exited on signal 0 (Unknown signal 0). -------------------------------------------------------------------------- mpirun: clean termination accomplished 6 total processes killed (some possibly by mpirun during cleanup) MMPBSA.py.MPI being run on 6 processors ptraj found! Using /net/bccs/cbu/linux64/amber11/bin/ptraj sander found! Using /net/bccs/cbu/linux64/amber11/bin/sander Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi) Preparing trajectories with ptraj... 32 frames were read in and processed by ptraj for use in calculation. Starting calculations Starting gb calculation... calculating ligand contribution... calculating receptor contribution... calculating complex contribution... Calculations complete. Writing output file(s)... Timing: Processing Trajectories With Ptraj: 7.102 min. Total GB Calculation Time (sander): 697.310 min. Output File Writing Time: 0.082 min. Total Time Taken: 711.157 min. MMPBSA Finished. Thank you for using. Please send any bugs/suggestions/comments to amber@ambermd.org ptraj found! Using /scratch/software/amber11/bin/ptraj sander found! Using /scratch/software/amber11/bin/sander Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi) Preparing trajectories with ptraj... Error! Ptraj failed. Check coordinate and topology files for the complex. NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files. ptraj found! Using /scratch/software/amber11/bin/ptraj sander found! Using /scratch/software/amber11/bin/sander Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi) Preparing trajectories with ptraj... MMPBSA.py.MPI being run on 6 processors ptraj found! Using /scratch/software/amber11/bin/ptraj sander found! Using /scratch/software/amber11/bin/sander Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi) Preparing trajectories with ptraj... 11 frames were read in and processed by ptraj for use in calculation. Starting calculations Starting gb calculation... calculating ligand contribution... calculating receptor contribution... calculating complex contribution... Calculations complete. Writing output file(s)... Timing: Processing Trajectories With Ptraj: 5.743 min. Total GB Calculation Time (sander): 152.027 min. Output File Writing Time: 0.042 min. Total Time Taken: 158.777 min. MMPBSA Finished. Thank you for using. Please send any bugs/suggestions/comments to amber@ambermd.org