CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 01/06/16 15:50:12 | Available memory: 175.605 MB INPUT: Reading Input from file pt-diheds.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [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 10] [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, 10 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 10 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 10 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'](0) Warning: dihedral: One or more masks have no atoms. Warning: Setup failed for [dihedral g1h4ph5p :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat ]: Skipping 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''](0) Warning: dihedral: One or more masks have no atoms. Warning: Setup failed for [dihedral g2h4ph5s :2@H4' :2@C4' :2@C5' :2@H5'' out diheds.dat ]: Skipping 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 (1-10, 1) ----- 0% 11% 22% 33% 44% 56% 67% 78% 89% 100% Complete. Read 10 frames and processed 10 frames. TIME: Trajectory processing: 0.2448 s TIME: Avg. throughput= 40.8560 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 10 c1c8 "c1c8" (double, torsion), size is 10 c2c4 "c2c4" (double, torsion), size is 10 c2c8 "c2c8" (double, torsion), size is 10 e1c4 "e1c4" (double, torsion), size is 10 e1c2 "e1c2" (double, torsion), size is 10 e1h3 "e1h3" (double, torsion), size is 10 b2 "b2" (double, torsion), size is 10 g1h4ph5p "g1h4ph5p" (double, torsion), size is 0 g2h4ph5s "g2h4ph5s" (double, torsion), size is 0 d1h3ph4p "d1h3ph4p" (double, torsion), size is 10 d2h3ph4p "d2h3ph4p" (double, torsion), size is 10 DATAFILES: diheds.dat (Standard Data File): c1c4 c1c8 c2c4 c2c8 ... g1h4ph5p g2h4ph5s d1h3ph4p d2h3ph4p Warning: Set 'g1h4ph5p' contains no data. Warning: Set 'g2h4ph5s' contains no data. ---------- RUN END --------------------------------------------------- TIME: Total execution time: 0.3466 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.