CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 01/06/16 16:04:58 | Available memory: 696.762 MB INPUT: Reading Input from file pt-diheds.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [parm ../../../../../A-form.pdb [striped]] Reading '../../../../../A-form.pdb' as PDB File A-form.pdb: determining bond info from distances. Warning: A-form.pdb: Determining default bond distances from element types. [reference ../../../../../A-form.pdb parm [striped] [a-form]] Reading '../../../../../A-form.pdb' as PDB [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18 start 1 stop 2] [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@N9 :2@C4 out diheds.dat ] DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N9]-[:2@C4] Output range is -180 to 180 degrees. [dihedral c2c8 :2@H1' :2@C1' :2@N9 :2@C8 out diheds.dat ] DIHEDRAL: [:2@H1']-[:2@C1']-[:2@N9]-[:2@C8] 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 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: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 2 frames 1: [striped] 'A-form.pdb', 65 atoms, 2 res, box: None, 1 mol INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 2 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 2 frames. REFERENCE FRAMES (1 total): 0: '../../../../../A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES Warning: Active reference has only 65 atoms, parm '[traj]' has 3301. Warning: Parm will only have reference coordinates for the first 65 atoms (distance-based masks only). ..................................................... ACTION SETUP FOR PARM '[traj]' (14 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 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@N9 :2@C4 out diheds.dat ] [:2@H1'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) 5: [dihedral c2c8 :2@H1' :2@C1' :2@N9 :2@C8 out diheds.dat ] [:2@H1'](1) [:2@C1'](1) [:2@N9](1) [:2@C8](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 g2h4ph5s :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 d1h3ph4p :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat ] [:1@H3'](1) [:1@C3'](1) [:1@C4'](1) [:1@H4'](1) 13: [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) ----- traj.1.01 (1-2, 1) ----- 0% 100% Complete. Read 2 frames and processed 2 frames. TIME: Trajectory processing: 0.0318 s TIME: Avg. throughput= 62.9426 frames / second. ACTION OUTPUT: DATASETS: 13 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../../A-form.pdb', refindex 0 (65 atoms) c1c4 "c1c4" (double, torsion), size is 2 c1c8 "c1c8" (double, torsion), size is 2 c2c4 "c2c4" (double, torsion), size is 2 c2c8 "c2c8" (double, torsion), size is 2 e1c4 "e1c4" (double, torsion), size is 2 e1c2 "e1c2" (double, torsion), size is 2 e1h3 "e1h3" (double, torsion), size is 2 b2 "b2" (double, torsion), size is 2 g1h4ph5p "g1h4ph5p" (double, torsion), size is 2 g2h4ph5s "g2h4ph5s" (double, torsion), size is 2 d1h3ph4p "d1h3ph4p" (double, torsion), size is 2 d2h3ph4p "d2h3ph4p" (double, torsion), size is 2 DATAFILES: diheds.dat (Standard Data File): c1c4 c1c8 c2c4 c2c8 ... g1h4ph5p g2h4ph5s d1h3ph4p d2h3ph4p ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.7333 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.