set_SCR: using existing PBS job directory /scratch/batch/50554 set_LSCR: using existing PBS job directory /scratch.local/batch/50554 set JOBID=`echo $PBS_JOBID | cut -d'.' -f1` echo 50554.ember cut -d. -f1 cd /scratch/batch/50554 saveafterjob tar cf mmpbsa_g1octa.50554.tar * cp /u/ac/cgaughan/mmpbsa_g1octa.in /scratch/batch/50554 cp /u/ac/cgaughan/g1octa.top /scratch/batch/50554 cp /u/ac/cgaughan/g1octa_nosolv.top /scratch/batch/50554 cp /u/ac/cgaughan/g1hexa_4octa_nosolv.top /scratch/batch/50554 cp /u/ac/cgaughan/g1dimer_4octa_nosolv.top /scratch/batch/50554 cp /u/ac/cgaughan/g1octa_combined_mdx /scratch/batch/50554 mpirun -np 16 /gpfs1/apps/chemistry/amber/amber11/bin/MMPBSA.py -O -i mmpbsa_g1octa.in -o G1OCTA_RESULTS_MMPBSA.dat -sp g1octa.top -cp g1octa_nosolv.top -rp g1hexa_4octa_nosolv.top -lp g1dimer_4octa_nosolv.top -y g1octa_combined_mdx MPI: ember-cmp2: 0x1bf000004d755309: Warning: igb=2 should be used with mbondi2 pbradii set. Yours are modified Bondi radii (mbondi) MPI: ember-cmp2: 0x1bf000004d755309: checkCoordinates(): Could not predict number of frames for AMBER trajectory file: _MMPBSA_receptor.mdcrd MPI: ember-cmp2: 0x1bf000004d755309: If this is not a compressed file then there is a problem MPI: ember-cmp2: 0x1bf000004d755309: checkCoordinates(): Could not predict number of frames for AMBER trajectory file: _MMPBSA_ligand.mdcrd MPI: ember-cmp2: 0x1bf000004d755309: If this is not a compressed file then there is a problem MPI: ember-cmp2: 0x1bf000004d755309: forrtl: severe (174): SIGSEGV, segmentation fault occurred MPI: ember-cmp2: 0x1bf000004d755309: Image PC Routine Line Source MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000450023 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 00000000006461B0 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 00000000004AADC4 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000049C998 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000049A3E5 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000495B0C Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000040954C Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: libc.so.6 00002B32A9223BC6 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000409449 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: forrtl: severe (174): SIGSEGV, segmentation fault occurred MPI: ember-cmp2: 0x1bf000004d755309: Image PC Routine Line Source MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000450023 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 00000000006461B0 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 00000000004AADC4 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000049C998 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000049A3E5 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000495B0C Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000040954C Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: libc.so.6 00002B5DBBFDCBC6 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000409449 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: forrtl: severe (174): SIGSEGV, segmentation fault occurred MPI: ember-cmp2: 0x1bf000004d755309: Image PC Routine Line Source MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000450023 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 00000000006461B0 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 00000000004AADC4 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000049C998 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000049A3E5 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000495B0C Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 000000000040954C Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: libc.so.6 00002B95FC241BC6 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: sander 0000000000409449 Unknown Unknown Unknown MPI: ember-cmp2: 0x1bf000004d755309: Error: Sander output is missing values! MPI: ember-cmp2: 0x1bf000004d755309: VDWAALS = ************* EEL = -5776.4965 EGB = -9434.5095 MPI: ember-cmp2: 0x1bf000004d755309: MPI: could not run executable (case #4)