CPPTRAJ: Trajectory Analysis. V14.05 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ INPUT: Reading Input from STDIN TIME: Total execution time: 0.0000 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095. CPPTRAJ: Trajectory Analysis. V14.05 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ INPUT: Reading Input from STDIN TIME: Total execution time: 0.0000 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095. CPPTRAJ: Trajectory Analysis. V14.05 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ INPUT: Reading Input from STDIN TIME: Total execution time: 0.0000 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095. CPPTRAJ: Trajectory Analysis. V14.05 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ INPUT: Reading Input from STDIN TIME: Total execution time: 0.0000 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095. CPPTRAJ: Trajectory Analysis. V14.05 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ INPUT: Reading Input from STDIN TIME: Total execution time: 0.0000 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095. CPPTRAJ: Trajectory Analysis. V14.05 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ INPUT: Reading Input from STDIN [parm D2B_VAC.prmtop [D2B]] Reading 'D2B_VAC.prmtop' as Amber Topology [trajin D2B_1.mdcrd 1 25000 10 [D2B]] Reading 'D2B_1.mdcrd' as Amber Trajectory [trajin D2B_2.mdcrd 1 25000 10 [D2B]] Reading 'D2B_2.mdcrd' as Amber Trajectory [trajin D2B_3.mdcrd 1 25000 10 [D2B]] Reading 'D2B_3.mdcrd' as Amber Trajectory [trajin D2B_4.mdcrd 1 25000 10 [D2B]] Reading 'D2B_4.mdcrd' as Amber Trajectory [trajin D2B_5.mdcrd 1 25000 10 [D2B]] Reading 'D2B_5.mdcrd' as Amber Trajectory [trajin D2B_6.mdcrd 1 25000 10 [D2B]] Reading 'D2B_6.mdcrd' as Amber Trajectory [trajin D2B_7.mdcrd 1 25000 10 [D2B]] Reading 'D2B_7.mdcrd' as Amber Trajectory [trajin D2B_8.mdcrd 1 25000 10 [D2B]] Reading 'D2B_8.mdcrd' as Amber Trajectory [trajin D2B_9.mdcrd 1 25000 10 [D2B]] Reading 'D2B_9.mdcrd' as Amber Trajectory [trajin D2B_10.mdcrd 1 25000 10 [D2B]] Reading 'D2B_10.mdcrd' as Amber Trajectory [trajin D2B_11.mdcrd 1 25000 10 [D2B]] Reading 'D2B_11.mdcrd' as Amber Trajectory [trajin D2B_12.mdcrd 1 25000 10 [D2B]] Reading 'D2B_12.mdcrd' as Amber Trajectory [trajin D2B_13.mdcrd 1 25000 10 [D2B]] Reading 'D2B_13.mdcrd' as Amber Trajectory [trajin D2B_14.mdcrd 1 25000 10 [D2B]] Reading 'D2B_14.mdcrd' as Amber Trajectory [trajin D2B_15.mdcrd 1 25000 10 [D2B]] Reading 'D2B_15.mdcrd' as Amber Trajectory [trajin D2B_16.mdcrd 1 25000 10 [D2B]] Reading 'D2B_16.mdcrd' as Amber Trajectory [trajin D2B_17.mdcrd 1 25000 10 [D2B]] Reading 'D2B_17.mdcrd' as Amber Trajectory [trajin D2B_18.mdcrd 1 25000 10 [D2B]] Reading 'D2B_18.mdcrd' as Amber Trajectory [trajin D2B_19.mdcrd 1 25000 10 [D2B]] Reading 'D2B_19.mdcrd' as Amber Trajectory [trajin D2B_20.mdcrd 1 25000 10 [D2B]] Reading 'D2B_20.mdcrd' as Amber Trajectory [readdata combined_qn.dat name QSext] Reading 'combined_qn.dat' as Standard Data File with name 'QSext' DataFile combined_qn.dat has 13 columns, 50001 lines. DataFile contains labels: 1: frame 2: qn 3: qn 4: qn 5: qn 6: qn 7: qn 8: qn 9: qn 10: qn 11: qn 12: qn 13: qn [cluster hieragglo clusters 100 averagelinkage data QSext out file_cnumvtime.dat summary file_summary.dat info file_info.dat summaryhalf halffile_summary.dat cpopvtime file_cpopvtime.dat repout file_REP repfmt pdb] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using 13 datasets. Hierarchical Agglomerative: 100 clusters, average-linkage. Cluster # vs time will be written to file_cnumvtime.dat Cluster pop vs time will be written to file_cpopvtime.dat Cluster information will be written to file_info.dat Summary of cluster results will be written to file_summary.dat Summary comparing parts of trajectory data for clusters will be written to halffile_summary.dat Frames will be split at the halfway point. Cluster representatives will be written to separate trajectories, prefix (file_REP), format PDB Warning: One or more analyses requested creation of default COORDS DataSet. CREATECRD: Saving coordinates from Top [D2B] to "_DEFAULTCRD_" ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [D2B] 'D2B_VAC.prmtop', 2683 atoms, 178 res, box: None, 1 mol, 50000 frames INPUT TRAJECTORIES: 0: 'D2B_1.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 1: 'D2B_2.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 2: 'D2B_3.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 3: 'D2B_4.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 4: 'D2B_5.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 5: 'D2B_6.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 6: 'D2B_7.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 7: 'D2B_8.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 8: 'D2B_9.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 9: 'D2B_10.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 10: 'D2B_11.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 11: 'D2B_12.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 12: 'D2B_13.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 13: 'D2B_14.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 14: 'D2B_15.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 15: 'D2B_16.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 16: 'D2B_17.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 17: 'D2B_18.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 18: 'D2B_19.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) 19: 'D2B_20.mdcrd' is an AMBER trajectory, Parm [D2B] (reading 2500 of 25000) Coordinate processing will occur on 50000 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[D2B]' (1 actions): 0: [createcrd _DEFAULTCRD_] ----- D2B_1.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_2.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_3.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_4.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_5.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_6.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_7.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_8.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_9.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_10.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_11.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_12.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_13.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_14.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_15.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_16.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_17.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_18.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_19.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- D2B_20.mdcrd (1-24991, 10) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. 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