CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/23/15 17:44:53 | Available memory: 14741.7 MB INPUT: Reading Input from file pt-analysis-pattern.in [parm ./pattern.pdb] Reading './pattern.pdb' as PDB File Determining bond info from distances. Warning: pattern.pdb: Determining default bond distances from element types. [trajin ./pattern.pdb] Reading './pattern.pdb' as PDB Read CRYST1 info from PDB: a=31.793 b=32.133 c=32.594 alpha=90 beta=90 gamma=90 Warning: Trajectory box type is 'Orthogonal' but topology box type is 'None'. Warning: Setting topology box information from trajectory. [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma out pattern_diheds_1.dat] DIHEDRAL: [:1@O5']-[:1@C5']-[:1@C4']-[:1@C3'] Output range is -180 to 180 degrees. [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta out pattern_diheds_1.dat] DIHEDRAL: [:1@C5']-[:1@C4']-[:1@C3']-[:1@O3'] Output range is -180 to 180 degrees. [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon out pattern_diheds_1.dat] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta out pattern_diheds_1.dat] DIHEDRAL: [:1@C3']-[:1@O3']-[:2@P]-[:2@O5'] Output range is -180 to 180 degrees. [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chin out pattern_diheds_1.dat] DIHEDRAL: [:1@O4']-[:1@C1']-[:1@N9]-[:1@C4] Output range is -180 to 180 degrees. [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha out pattern_diheds_2.dat] DIHEDRAL: [:1@O3']-[:2@P]-[:2@O5']-[:2@C5'] Output range is -180 to 180 degrees. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta out pattern_diheds_2.dat] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma out pattern_diheds_2.dat] DIHEDRAL: [:2@O5']-[:2@C5']-[:2@C4']-[:2@C3'] Output range is -180 to 180 degrees. [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta out pattern_diheds_2.dat] DIHEDRAL: [:2@C5']-[:2@C4']-[:2@C3']-[:2@O3'] Output range is -180 to 180 degrees. [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chin out pattern_diheds_2.dat] DIHEDRAL: [:2@O4']-[:2@C1']-[:2@N9]-[:2@C4] Output range is -180 to 180 degrees. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: pattern.pdb, 76 atoms, 13 res, box: Orthogonal, 12 mol INPUT TRAJECTORIES: 0: 'pattern.pdb' is a PDB file, Parm pattern.pdb (Orthogonal box) (reading 1 of 1) Coordinate processing will occur on 1 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'pattern.pdb' (10 actions): 0: [dihedral g1 :1@O5' :1@C5' :1@C4' :1@C3' type gamma out pattern_diheds_1.dat] [:1@O5'](1) [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) 1: [dihedral d1 :1@C5' :1@C4' :1@C3' :1@O3' type delta out pattern_diheds_1.dat] [:1@C5'](1) [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) 2: [dihedral e1 :1@C4' :1@C3' :1@O3' :2@P type epsilon out pattern_diheds_1.dat] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 3: [dihedral z1 :1@C3' :1@O3' :2@P :2@O5' type zeta out pattern_diheds_1.dat] [:1@C3'](1) [:1@O3'](1) [:2@P](1) [:2@O5'](1) 4: [dihedral c1 :1@O4' :1@C1' :1@N9 :1@C4 type chin out pattern_diheds_1.dat] [:1@O4'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 5: [dihedral a2 :1@O3' :2@P :2@O5' :2@C5' type alpha out pattern_diheds_2.dat] [:1@O3'](1) [:2@P](1) [:2@O5'](1) [:2@C5'](1) 6: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' type beta out pattern_diheds_2.dat] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 7: [dihedral g2 :2@O5' :2@C5' :2@C4' :2@C3' type gamma out pattern_diheds_2.dat] [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) 8: [dihedral d2 :2@C5' :2@C4' :2@C3' :2@O3' type delta out pattern_diheds_2.dat] [:2@C5'](1) [:2@C4'](1) [:2@C3'](1) [:2@O3'](1) 9: [dihedral c2 :2@O4' :2@C1' :2@N9 :2@C4 type chin out pattern_diheds_2.dat] [:2@O4'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) ----- pattern.pdb (1-1, 1) ----- Read CRYST1 info from PDB: a=31.793 b=32.133 c=32.594 alpha=90 beta=90 gamma=90 100% Complete. Read 1 frames and processed 1 frames. TIME: Trajectory processing: 0.0006 s TIME: Avg. throughput= 1782.5312 frames / second. ACTION OUTPUT: DATASETS: 11 data sets: pattern.pdb "pattern.pdb" (topology), size is 76 pattern.pdb, 76 atoms, 13 res, box: Orthogonal, 12 mol g1 "g1" (double, torsion(gamma)), size is 1 d1 "d1" (double, torsion(delta)), size is 1 e1 "e1" (double, torsion(epsilon)), size is 1 z1 "z1" (double, torsion(zeta)), size is 1 c1 "c1" (double, torsion(chin)), size is 1 a2 "a2" (double, torsion(alpha)), size is 1 b2 "b2" (double, torsion(beta)), size is 1 g2 "g2" (double, torsion(gamma)), size is 1 d2 "d2" (double, torsion(delta)), size is 1 c2 "c2" (double, torsion(chin)), size is 1 DATAFILES: pattern_diheds_1.dat (Standard Data File): g1 d1 e1 z1 c1 pattern_diheds_2.dat (Standard Data File): a2 b2 g2 d2 c2 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.0149 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.