CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/31/15 16:03:39 | Available memory: 1367.49 MB INPUT: Reading Input from file pt-jcoupling.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [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 ] [dihedral chi1_c4 :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 chi1_c8 :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 chi2_c4 :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 chi2_c8 :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 ep1_c4 :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 ep1_c2 :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 ep1_h3 :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 beta2 :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 gamma1 :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 delta1 :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 delta2 :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. [jcoupling name jcoup :1-2 out jcoupling.dat] Info: Using parameter file defined by $KARPLUS environment variable. J-COUPLING: Searching for dihedrals in mask [:1-2]. Using Karplus parameters in "./Karplus.txt" 21 parameters found for 4 residues. DataSets will be written to jcoupling.dat # Citations: Chou et al. JACS (2003) 125 p.8959-8966 # Perez et al. JACS (2001) 123 p.7081-7093 [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 50000 frames. TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (13 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [dihedral chi1_c4 :1@H1' :1@C1' :1@N9 :1@C4 out diheds.dat ] [:1@H1'](1) [:1@C1'](1) [:1@N9](1) [:1@C4](1) 2: [dihedral chi1_c8 :1@H1' :1@C1' :1@N9 :1@C8 out diheds.dat] [:1@H1'](1) [:1@C1'](1) [:1@N9](1) [:1@C8](1) 3: [dihedral chi2_c4 :2@H1' :2@C1' :2@N9 :2@C4 out diheds.dat] [:2@H1'](1) [:2@C1'](1) [:2@N9](1) [:2@C4](1) 4: [dihedral chi2_c8 :2@H1' :2@C1' :2@N9 :2@C8 out diheds.dat] [:2@H1'](1) [:2@C1'](1) [:2@N9](1) [:2@C8](1) 5: [dihedral ep1_c4 :1@C4' :1@C3' :1@O3' :2@P out diheds.dat] [:1@C4'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 6: [dihedral ep1_c2 :1@C2' :1@C3' :1@O3' :2@P out diheds.dat] [:1@C2'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 7: [dihedral ep1_h3 :1@H3' :1@C3' :1@O3' :2@P out diheds.dat] [:1@H3'](1) [:1@C3'](1) [:1@O3'](1) [:2@P](1) 8: [dihedral beta2 :2@P :2@O5' :2@C5' :2@C4' out diheds.dat] [:2@P](1) [:2@O5'](1) [:2@C5'](1) [:2@C4'](1) 9: [dihedral gamma1 :1@H4' :1@C4' :1@C5' :1@H5' out diheds.dat] [:1@H4'](1) [:1@C4'](1) [:1@C5'](1) [:1@H5'](1) 10: [dihedral delta1 :1@H3' :1@C3' :1@C4' :1@H4' out diheds.dat] [:1@H3'](1) [:1@C3'](1) [:1@C4'](1) [:1@H4'](1) 11: [dihedral delta2 :2@H3' :2@C3' :2@C4' :2@H4' out diheds.dat] [:2@H3'](1) [:2@C3'](1) [:2@C4'](1) [:2@H4'](1) 12: [jcoupling name jcoup :1-2 out jcoupling.dat] Warning: Atom 'P ' at position 3 not found for residue 3 Warning: Atom 'P ' at position 3 not found for residue 3 Warning: Atom 'P ' at position 3 not found for residue 3 J-COUPLING: [:1-2] Will calculate J-coupling for 11 dihedrals. ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 597.3188 s TIME: Avg. throughput= 83.7074 frames / second. ACTION OUTPUT: DATASETS: 22 data sets: chi1_c4 "chi1_c4" (double, torsion), size is 50000 chi1_c8 "chi1_c8" (double, torsion), size is 50000 chi2_c4 "chi2_c4" (double, torsion), size is 50000 chi2_c8 "chi2_c8" (double, torsion), size is 50000 ep1_c4 "ep1_c4" (double, torsion), size is 50000 ep1_c2 "ep1_c2" (double, torsion), size is 50000 ep1_h3 "ep1_h3" (double, torsion), size is 50000 beta2 "beta2" (double, torsion), size is 50000 gamma1 "gamma1" (double, torsion), size is 50000 delta1 "delta1" (double, torsion), size is 50000 delta2 "delta2" (double, torsion), size is 50000 jcoup:1 "A5:1_H1'-C1'-N9-C4" (float), size is 50000 jcoup:2 "A5:1_H1'-C1'-N9-C8" (float), size is 50000 jcoup:3 "A5:1_C4'-C3'-O3'-P" (float), size is 50000 jcoup:4 "A5:1_C2'-C3'-O3'-P" (float), size is 50000 jcoup:5 "A5:1_H3'-C3'-O3'-P" (float), size is 50000 jcoup:6 "A5:1_H4'-C4'-C5'-H5'" (float), size is 50000 jcoup:7 "A5:1_H3'-C3'-C4'-H4'" (float), size is 50000 jcoup:8 "A3:2_H1'-C1'-N9-C4" (float), size is 50000 jcoup:9 "A3:2_H1'-C1'-N9-C8" (float), size is 50000 jcoup:10 "A3:2_P-O5'-C5'-C4'" (float), size is 50000 jcoup:11 "A3:2_H3'-C3'-C4'-H4'" (float), size is 50000 DATAFILES: diheds.dat (Standard Data File): chi1_c4 chi1_c8 chi2_c4 chi2_c8 ... beta2 gamma1 delta1 delta2 jcoupling.dat (Standard Data File): A5:1_H1'-C1'-N9-C4 A5:1_H1'-C1'-N9-C8 A5:1_C4'-C3'-O3'-P A5:1_C2'-C3'-O3'-P ... A3:2_H1'-C1'-N9-C4 A3:2_H1'-C1'-N9-C8 A3:2_P-O5'-C5'-C4' A3:2_H3'-C3'-C4'-H4' ---------- RUN END --------------------------------------------------- [avg jcoup out avg-jcoupling.dat] AVERAGE: Calculating average of 11 data sets. Writing results to avg-jcoupling.dat ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 1 analyses: 0: [avg jcoup out avg-jcoupling.dat] TIME: Analyses took 0.0127 seconds. DATASETS: 22 data sets: chi1_c4 "chi1_c4" (double, torsion), size is 50000 chi1_c8 "chi1_c8" (double, torsion), size is 50000 chi2_c4 "chi2_c4" (double, torsion), size is 50000 chi2_c8 "chi2_c8" (double, torsion), size is 50000 ep1_c4 "ep1_c4" (double, torsion), size is 50000 ep1_c2 "ep1_c2" (double, torsion), size is 50000 ep1_h3 "ep1_h3" (double, torsion), size is 50000 beta2 "beta2" (double, torsion), size is 50000 gamma1 "gamma1" (double, torsion), size is 50000 delta1 "delta1" (double, torsion), size is 50000 delta2 "delta2" (double, torsion), size is 50000 jcoup:1 "A5:1_H1'-C1'-N9-C4" (float), size is 50000 jcoup:2 "A5:1_H1'-C1'-N9-C8" (float), size is 50000 jcoup:3 "A5:1_C4'-C3'-O3'-P" (float), size is 50000 jcoup:4 "A5:1_C2'-C3'-O3'-P" (float), size is 50000 jcoup:5 "A5:1_H3'-C3'-O3'-P" (float), size is 50000 jcoup:6 "A5:1_H4'-C4'-C5'-H5'" (float), size is 50000 jcoup:7 "A5:1_H3'-C3'-C4'-H4'" (float), size is 50000 jcoup:8 "A3:2_H1'-C1'-N9-C4" (float), size is 50000 jcoup:9 "A3:2_H1'-C1'-N9-C8" (float), size is 50000 jcoup:10 "A3:2_P-O5'-C5'-C4'" (float), size is 50000 jcoup:11 "A3:2_H3'-C3'-C4'-H4'" (float), size is 50000 DATAFILES: diheds.dat (Standard Data File): chi1_c4 chi1_c8 chi2_c4 chi2_c8 ... beta2 gamma1 delta1 delta2 jcoupling.dat (Standard Data File): A5:1_H1'-C1'-N9-C4 A5:1_H1'-C1'-N9-C8 A5:1_C4'-C3'-O3'-P A5:1_C2'-C3'-O3'-P ... A3:2_H1'-C1'-N9-C4 A3:2_H1'-C1'-N9-C8 A3:2_P-O5'-C5'-C4' A3:2_H3'-C3'-C4'-H4' avg-jcoupling.dat (DataSet Average) ---------- RUN END --------------------------------------------------- TIME: Total execution time: 599.2190 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.