CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/03/15 15:34:51 | Available memory: 53215.3 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.c2] Reading '../ctraj.c2' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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', 67 atoms, 2 res, box: Orthogonal, 1 mol, 116495 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 116495 of 116495) Coordinate processing will occur on 116495 frames. TIME: Run Initialization took 0.0006 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c2 (1-116495, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 101 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@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N2' 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@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N2' 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@O6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N2' 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@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@C4' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' 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@O6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' 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@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 116495 frames and processed 116495 frames. TIME: Trajectory processing: 0.7710 s TIME: Avg. throughput= 151098.9189 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 90.1249 101 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 115556 0.992 4.62 0.677 2 :1@N9_:2@C5 115424 0.991 4.75 0.667 3 :1@N9_:2@N9 115257 0.989 5.27 0.617 4 :1@N9_:2@N7 114545 0.983 5.05 0.741 5 :1@C4_:2@C6 114510 0.983 4.45 0.793 6 :1@C4_:2@C4 114368 0.982 4.95 0.647 7 :1@C4_:2@O6 114201 0.98 4.65 0.869 8 :1@N9_:2@C8 113519 0.974 5.28 0.779 9 :1@N9_:2@C4 113430 0.974 4.82 0.554 10 :1@C4_:2@N7 113176 0.972 4.93 0.852 11 :1@N3_:2@C5 113051 0.97 4.73 0.729 12 :1@C4_:2@N9 112761 0.968 5.5 0.746 13 :1@C5_:2@C5 112686 0.967 4.79 0.869 14 :1@N3_:2@C6 112245 0.964 4.57 0.796 15 :1@N9_:2@C6 112065 0.962 4.77 0.82 16 :1@C5_:2@C6 111964 0.961 4.35 0.873 17 :1@N3_:2@O6 111786 0.96 4.68 0.874 18 :1@C5_:2@O6 111284 0.955 4.38 1.02 19 :1@N3_:2@C4 110984 0.953 5.15 0.615 20 :1@C6_:2@O6 110947 0.952 4.28 1.1 21 :1@C8_:2@C4 110765 0.951 5.01 0.697 22 :1@N9_:2@N3 110716 0.95 4.96 0.698 23 :1@C8_:2@N3 109548 0.94 5.06 0.744 24 :1@C5_:2@C4 109460 0.94 5.17 0.805 25 :1@C4_:2@N1 109422 0.939 4.49 0.875 26 :1@C6_:2@C6 109408 0.939 4.47 0.938 27 :1@C5_:2@N1 109315 0.938 4.35 0.847 28 :1@C8_:2@C5 109107 0.937 4.87 0.832 29 :1@N7_:2@N1 109004 0.936 4.59 1.05 30 :1@N1_:2@O6 108879 0.935 4.25 0.986 31 :1@N1_:2@C6 108460 0.931 4.55 0.859 32 :1@C2_:2@C6 108366 0.93 4.54 0.774 33 :1@N3_:2@N1 108268 0.929 4.73 0.984 34 :1@N3_:2@N7 108252 0.929 4.85 0.932 35 :1@C4_:2@C8 108185 0.929 5.33 0.89 36 :1@C8_:2@C2 107930 0.926 4.9 0.984 37 :1@N9_:2@O6 107795 0.925 5.11 0.837 38 :1@C8_:2@C6 107782 0.925 4.79 0.995 39 :1@C4_:2@N3 107468 0.923 5.03 0.604 40 :1@C2_:2@N1 107406 0.922 4.76 0.953 41 :1@C2_:2@O6 107301 0.921 4.36 0.871 42 :1@N9_:2@C2 107203 0.92 4.87 0.899 43 :1@N7_:2@C6 107081 0.919 4.57 0.948 44 :1@N9_:2@N1 107060 0.919 4.77 0.915 45 :1@C8_:2@N1 106788 0.917 4.77 1.06 46 :1@N7_:2@C2 106760 0.916 4.86 0.909 47 :1@C4_:2@C2 106597 0.915 4.76 0.802 48 :1@N7_:2@C4 106551 0.915 5.21 0.797 49 :1@N3_:2@N3 106537 0.915 5.35 0.767 50 :1@N3_:2@N9 106164 0.911 5.61 0.687 51 :1@C6_:2@N1 106132 0.911 4.44 0.737 52 :1@C2_:2@C5 105934 0.909 4.91 0.764 53 :1@C5_:2@C2 105890 0.909 4.74 0.684 54 :1@N7_:2@N3 105697 0.907 5.21 0.788 55 :1@C8_:2@N9 105630 0.907 5.45 0.783 56 :1@N1_:2@N1 105536 0.906 4.64 0.79 57 :1@C6_:2@C5 105166 0.903 5.08 0.97 58 :1@C5_:2@N3 105072 0.902 5.19 0.654 59 :1@N1_:2@C5 104165 0.894 5.13 0.9 60 :1@N7_:2@C5 104010 0.893 4.85 0.766 61 :1@N3_:2@C8 103933 0.892 5.33 0.943 62 :1@O6_:2@N1 103509 0.889 4.77 0.887 63 :1@C2_:2@C4 103295 0.887 5.53 0.656 64 :1@N3_:2@C2 103101 0.885 5.02 0.992 65 :1@C6_:2@C2 103034 0.884 5.05 0.716 66 :1@C8_:2@N7 102674 0.881 5.16 0.886 67 :1@C5_:2@N7 102633 0.881 5.07 0.851 68 :1@O6_:2@O6 101850 0.874 4.39 1.04 69 :1@O6_:2@C6 101222 0.869 4.77 0.953 70 :1@N2_:2@C6 101160 0.868 4.9 0.87 71 :1@C2_:2@N7 101084 0.868 5.06 1.06 72 :1@C5_:2@N2 100982 0.867 5.07 0.809 73 :1@C2_:2@C2 100480 0.863 5.24 0.957 74 :1@N2_:2@O6 100418 0.862 4.59 0.98 75 :1@C8_:2@C8 100391 0.862 5.45 0.885 76 :1@N1_:2@C2 100208 0.86 5.27 0.794 77 :1@N7_:2@O6 99952 0.858 4.54 1 78 :1@N7_:2@N7 98849 0.849 5.25 0.886 79 :1@N2_:2@N1 98183 0.843 5.16 1.08 80 :1@N7_:2@N2 98081 0.842 5.02 0.999 81 :1@C2_:2@N3 97853 0.84 5.71 0.719 82 :1@N2_:2@C5 97611 0.838 5.27 0.82 83 :1@C6_:2@C4 96729 0.83 5.57 0.918 84 :1@C8_:2@O6 96697 0.83 4.9 0.992 85 :1@N1_:2@C4 96574 0.829 5.75 0.824 86 :1@C4_:2@N2 96295 0.827 5.08 0.913 87 :1@C5_:2@N9 95271 0.818 5.72 0.926 88 :1@C8_:2@N2 95261 0.818 5.07 1.08 89 :1@C6_:2@N7 94128 0.808 5.34 0.9 90 :1@C5_:2@C8 94058 0.807 5.58 0.917 91 :1@N7_:2@N9 93343 0.801 5.7 0.93 92 :1@N1_:2@N7 92149 0.791 5.29 1.02 93 :1@N9_:2@N2 91004 0.781 5.05 0.797 94 :1@N2_:2@C4 88516 0.76 5.91 0.656 95 :1@O6_:2@C5 88488 0.76 5.38 0.913 96 :1@N7_:2@C8 87795 0.754 5.62 0.916 97 :1@N2_:2@N7 86679 0.744 5.12 1.03 98 :1@C2_:2@N9 85994 0.738 5.99 0.76 99 :1@C2_:2@C8 84961 0.729 5.57 0.98 100 :1@N3_:2@N2 83551 0.717 5.09 1.12 101 :1@N2_:2@C8 70533 0.605 5.66 0.922 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0059 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 116495 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 116495 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 116495 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 116495 COM "COM" (double, distance), size is 116495 v_base1 "v_base1" (vector), size is 116495 v_base2 "v_base2" (vector), size is 116495 normalangle "normalangle" (double), size is 116495 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: 0.9915 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.