CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:02:27 | Available memory: 54712.5 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c0] Reading '../ctraj.c0' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9', contacts set up based on first frame. Distance cutoff is 7 Angstroms, imaging is on. Mask selection will not include solvent. Data set name: Contacts_00001 Saving minimum observed distances in set 'Contacts_00001[mindist]' Contact stats will be written to 'STDOUT' Contact res pairs will be written to 'STDOUT' [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] VECTORMATH: Calculating Angle from dot product of vectors v_base1 and v_base2 Vectors will be normalized. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 161463 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 161463 of 161463) Coordinate processing will occur on 161463 frames. TIME: Run Initialization took 0.0007 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](41) Reference mask: [:1,2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c0 (1-161463, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 92 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@N6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@N9' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@N6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@N9' Atom ':1@N7' to ':2@C8' Atom ':1@N7' to ':2@N7' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@N6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C4' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@N9' Atom ':1@C6' to ':2@C8' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@N9' Atom ':1@N6' to ':2@C8' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C4' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N6' Atom ':1@C2' to ':2@C4' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@C8' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 161463 frames and processed 161463 frames. TIME: Trajectory processing: 0.9826 s TIME: Avg. throughput= 164321.5375 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 87.7921 92 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 160924 0.997 4.29 0.597 2 :1@C4_:2@C6 160718 0.995 4.52 0.607 3 :1@C4_:2@C4 160591 0.995 4.41 0.553 4 :1@C5_:2@C6 160474 0.994 4.16 0.678 5 :1@N3_:2@C4 160268 0.993 4.39 0.581 6 :1@N3_:2@C5 160260 0.993 4.55 0.638 7 :1@C5_:2@C5 160170 0.992 4.26 0.695 8 :1@N9_:2@C5 159838 0.99 4.57 0.702 9 :1@C4_:2@N9 159707 0.989 4.71 0.58 10 :1@C5_:2@N1 159479 0.988 4.27 0.729 11 :1@N3_:2@C6 159477 0.988 4.99 0.686 12 :1@C2_:2@C4 159471 0.988 4.36 0.693 13 :1@N9_:2@C4 159372 0.987 4.93 0.665 14 :1@N3_:2@N9 159328 0.987 4.49 0.633 15 :1@C6_:2@N1 159293 0.987 4.13 0.676 16 :1@C4_:2@N1 159161 0.986 4.81 0.73 17 :1@C5_:2@C4 159154 0.986 4.47 0.634 18 :1@C4_:2@N3 159009 0.985 4.73 0.74 19 :1@C6_:2@C6 158967 0.985 4.28 0.738 20 :1@N1_:2@C4 158941 0.984 4.45 0.68 21 :1@N3_:2@N3 158813 0.984 4.66 0.705 22 :1@N9_:2@C6 158782 0.983 4.81 0.731 23 :1@C4_:2@N6 158732 0.983 4.96 0.667 24 :1@C2_:2@C5 158662 0.983 4.69 0.783 25 :1@C4_:2@N7 158660 0.983 4.49 0.824 26 :1@C5_:2@N6 158612 0.982 4.47 0.759 27 :1@C6_:2@C5 158589 0.982 4.49 0.75 28 :1@C6_:2@C4 158404 0.981 4.48 0.609 29 :1@N9_:2@N9 158376 0.981 5.14 0.645 30 :1@C5_:2@C2 158304 0.98 4.43 0.834 31 :1@N7_:2@C6 158137 0.979 4.24 0.877 32 :1@C4_:2@C8 158062 0.979 4.72 0.787 33 :1@C4_:2@C2 157747 0.977 4.83 0.83 34 :1@N3_:2@N1 157717 0.977 5.21 0.79 35 :1@C5_:2@N3 157697 0.977 4.58 0.771 36 :1@C6_:2@N3 157658 0.976 4.31 0.667 37 :1@N6_:2@N1 157601 0.976 4.14 0.752 38 :1@N3_:2@N7 157522 0.976 4.73 0.807 39 :1@N1_:2@N1 157483 0.975 4.51 0.786 40 :1@N7_:2@C5 157270 0.974 4.53 0.829 41 :1@C8_:2@C5 157188 0.974 4.66 0.851 42 :1@N1_:2@C5 157166 0.973 4.69 0.819 43 :1@N3_:2@C2 157161 0.973 5 0.81 44 :1@C2_:2@N9 157126 0.973 4.59 0.696 45 :1@N3_:2@C8 156851 0.971 4.66 0.794 46 :1@C2_:2@C6 156462 0.969 4.97 0.825 47 :1@N1_:2@C6 156384 0.969 4.69 0.845 48 :1@N7_:2@N1 156286 0.968 4.45 0.957 49 :1@C5_:2@N7 156027 0.966 4.71 0.856 50 :1@C5_:2@N9 156007 0.966 5.04 0.609 51 :1@N9_:2@N7 155961 0.966 4.48 0.845 52 :1@C8_:2@C6 155767 0.965 4.57 0.886 53 :1@N6_:2@C6 155592 0.964 4.49 0.824 54 :1@N1_:2@N9 155353 0.962 4.95 0.649 55 :1@C6_:2@N9 155169 0.961 5.16 0.6 56 :1@N9_:2@C8 155028 0.96 4.82 0.795 57 :1@C6_:2@N6 154883 0.959 4.71 0.841 58 :1@N7_:2@N6 154846 0.959 4.2 0.899 59 :1@N9_:2@N6 154831 0.959 5 0.76 60 :1@N6_:2@C4 154445 0.957 5 0.652 61 :1@C2_:2@C8 154240 0.955 5.02 0.827 62 :1@N7_:2@C4 153942 0.953 4.97 0.776 63 :1@C5_:2@C8 153585 0.951 5.12 0.758 64 :1@C2_:2@N7 153560 0.951 5.1 0.876 65 :1@C8_:2@C4 153231 0.949 5.17 0.784 66 :1@N6_:2@C5 152778 0.946 4.95 0.788 67 :1@C8_:2@N7 152167 0.942 4.7 0.921 68 :1@N7_:2@N7 152108 0.942 4.87 0.914 69 :1@N3_:2@N6 151995 0.941 5.56 0.723 70 :1@C8_:2@N6 151599 0.939 4.49 0.893 71 :1@C6_:2@N7 151047 0.935 5.11 0.865 72 :1@N6_:2@N6 150714 0.933 4.77 0.972 73 :1@N9_:2@N3 150150 0.93 5.34 0.821 74 :1@N7_:2@C2 150080 0.93 4.81 0.972 75 :1@N9_:2@N1 149640 0.927 5.21 0.785 76 :1@N1_:2@N7 149281 0.925 5.29 0.913 77 :1@N1_:2@C8 148935 0.922 5.41 0.803 78 :1@C6_:2@C8 148476 0.92 5.44 0.742 79 :1@N7_:2@N3 148056 0.917 5.12 0.886 80 :1@C8_:2@N1 147679 0.915 4.93 0.909 81 :1@C8_:2@N9 146789 0.909 5.55 0.716 82 :1@C8_:2@C8 146720 0.909 5.24 0.792 83 :1@N7_:2@N9 145658 0.902 5.55 0.715 84 :1@N1_:2@N6 145162 0.899 5.22 0.922 85 :1@N6_:2@N9 142804 0.884 5.79 0.601 86 :1@N7_:2@C8 142615 0.883 5.42 0.762 87 :1@N9_:2@C2 141272 0.875 5.32 0.86 88 :1@C2_:2@N6 139356 0.863 5.52 0.854 89 :1@C8_:2@N3 137600 0.852 5.42 0.855 90 :1@C8_:2@C2 136348 0.844 5.22 0.912 91 :1@N6_:2@N7 133598 0.827 5.61 0.867 92 :1@N6_:2@C8 118030 0.731 5.95 0.685 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0121 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 161463 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 161463 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 161463 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 161463 COM "COM" (double, distance), size is 161463 v_base1 "v_base1" (vector), size is 161463 v_base2 "v_base2" (vector), size is 161463 normalangle "normalangle" (double), size is 161463 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 1.3639 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.