CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 11:40:07 | Available memory: 1.839 GB INPUT: Reading input from 'pt-diheds.in' [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c3] Reading '../ctraj.c3' as Amber NetCDF [dihedral c1c4 :1@H1' :1@C1' :1@N9 :1@C4 out diheds.dat] DIHEDRAL: [:1@H1']-[:1@C1']-[:1@N9]-[:1@C4] Output range is -180 to 180 degrees. [dihedral c1c8 :1@H1' :1@C1' :1@N9 :1@C8 out diheds.dat] DIHEDRAL: [:1@H1']-[:1@C1']-[:1@N9]-[:1@C8] Output range is -180 to 180 degrees. [dihedral c2c4 :2@H1' :2@C1' :2@N1 :2@C2 out diheds.dat] DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N1]-[:2@C2] Output range is -180 to 180 degrees. [dihedral c2c8 :2@H1' :2@C1' :2@N1 :2@C6 out diheds.dat] DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N1]-[:2@C6] Output range is -180 to 180 degrees. [dihedral e1c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat] DIHEDRAL: [:1@C4']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral e1c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat] DIHEDRAL: [:1@C2']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral e1h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat] DIHEDRAL: [:1@H3']-[:1@C3']-[:1@O3']-[:2@P] Output range is -180 to 180 degrees. [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat] DIHEDRAL: [:2@P]-[:2@O5']-[:2@C5']-[:2@C4'] Output range is -180 to 180 degrees. [dihedral g1h4ph5p :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat] DIHEDRAL: [:1@H4']-[:1@C4']-[:1@C5']-[:1@H5'] Output range is -180 to 180 degrees. [dihedral g2h4ph5p :2@H4' :2@C4' :2@C5' :2@H5' out diheds.dat] DIHEDRAL: [:2@H4']-[:2@C4']-[:2@C5']-[:2@H5'] Output range is -180 to 180 degrees. [dihedral g1h4ph5s :1@H4' :1@C4' :1@C5' :1@H5'' out diheds.dat] DIHEDRAL: [:1@H4']-[:1@C4']-[:1@C5']-[:1@H5''] Output range is -180 to 180 degrees. [dihedral g2h4ph5s :2@H4' :2@C4' :2@C5' :2@H5'' out diheds.dat] DIHEDRAL: [:2@H4']-[:2@C4']-[:2@C5']-[:2@H5''] Output range is -180 to 180 degrees. [dihedral d1h3ph4p :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat] DIHEDRAL: [:1@H3']-[:1@C3']-[:1@C4']-[:1@H4'] Output range is -180 to 180 degrees. [dihedral d2h3ph4p :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat] DIHEDRAL: [:2@H3']-[:2@C3']-[:2@C4']-[:2@H4'] Output range is -180 to 180 degrees. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: noWAt.topo.hmr, 63 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 49141 of 49141) Coordinate processing will occur on 49141 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (16 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [dihedral c1c4 :1@H1' :1@C1' :1@N9 :1@C4 out diheds.dat] [:1@H1'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 3: [dihedral c1c8 :1@H1' :1@C1' :1@N9 :1@C8 out diheds.dat] [:1@H1'](1) [:1@C1'](1) [:1@N9](1) [:1@C8](1) 4: [dihedral c2c4 :2@H1' :2@C1' :2@N1 :2@C2 out diheds.dat] [:2@H1'](1) [:2@C1'](1) [:2@N1](1) [:2@C2](1) 5: [dihedral c2c8 :2@H1' :2@C1' :2@N1 :2@C6 out diheds.dat] [:2@H1'](1) [:2@C1'](1) [:2@N1](1) [:2@C6](1) 6: [dihedral e1c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 7: [dihedral e1c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat] [:1@C2'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 8: [dihedral e1h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat] [:1@H3'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 9: [dihedral b2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 10: [dihedral g1h4ph5p :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat] [:1@H4'](1) [:1@C4'](1) [:1@C5'](1) [:1@H5'](1) 11: [dihedral g2h4ph5p :2@H4' :2@C4' :2@C5' :2@H5' out diheds.dat] [:2@H4'](1) [:2@C4'](1) [:2@C5'](1) [:2@H5'](1) 12: [dihedral g1h4ph5s :1@H4' :1@C4' :1@C5' :1@H5'' out diheds.dat] [:1@H4'](1) [:1@C4'](1) [:1@C5'](1) [:1@H5''](1) 13: [dihedral g2h4ph5s :2@H4' :2@C4' :2@C5' :2@H5'' out diheds.dat] [:2@H4'](1) [:2@C4'](1) [:2@C5'](1) [:2@H5''](1) 14: [dihedral d1h3ph4p :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat] [:1@H3'](1) [:1@C3'](1) [:1@C4'](1) [:1@H4'](1) 15: [dihedral d2h3ph4p :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat] [:2@H3'](1) [:2@C3'](1) [:2@C4'](1) [:2@H4'](1) ----- ctraj.c3 (1-49141, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 49141 frames and processed 49141 frames. TIME: Avg. throughput= 165627.4436 frames / second. ACTION OUTPUT: DATASETS (14 total): c1c4 "c1c4" (double, torsion), size is 49141 c1c8 "c1c8" (double, torsion), size is 49141 c2c4 "c2c4" (double, torsion), size is 49141 c2c8 "c2c8" (double, torsion), size is 49141 e1c4 "e1c4" (double, torsion), size is 49141 e1c2 "e1c2" (double, torsion), size is 49141 e1h3 "e1h3" (double, torsion), size is 49141 b2 "b2" (double, torsion), size is 49141 g1h4ph5p "g1h4ph5p" (double, torsion), size is 49141 g2h4ph5p "g2h4ph5p" (double, torsion), size is 49141 g1h4ph5s "g1h4ph5s" (double, torsion), size is 49141 g2h4ph5s "g2h4ph5s" (double, torsion), size is 49141 d1h3ph4p "d1h3ph4p" (double, torsion), size is 49141 d2h3ph4p "d2h3ph4p" (double, torsion), size is 49141 DATAFILES (1 total): diheds.dat (Standard Data File): c1c4 c1c8 c2c4 c2c8 ... g1h4ph5s g2h4ph5s d1h3ph4p d2h3ph4p RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 0.2967 s ( 22.49%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 1.0224 s ( 77.50%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.3192 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 1.3311 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.