CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:28:43 | Available memory: 1.215 GB INPUT: Reading input from '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-] Warning: Action specified before trajin/ensemble. Assuming trajin. 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*). Best-fit RMSD will be calculated, coords will be rotated and translated. [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_00002 Saving minimum observed distances in set 'Contacts_00002[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 (1 total): 0: [traj] noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 144474 of 144474) Coordinate processing will occur on 144474 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: 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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c2 (1-144474, 1) ----- 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 118 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@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@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@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@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@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@O6' to ':2@N9' Atom ':1@O6' to ':2@C8' Atom ':1@O6' to ':2@N7' 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@O6' to ':2@C2' Atom ':1@O6' to ':2@N2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' 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@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' Atom ':1@N1' to ':2@N3' 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@N2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N9' 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@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 144474 frames and processed 144474 frames. TIME: Avg. throughput= 82358.8631 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 112.791 118 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 143922 0.996 4.23 0.557 2 :1@C4_:2@C4 143592 0.994 4.31 0.483 3 :1@C4_:2@C8 143493 0.993 4.07 0.663 4 :1@N9_:2@N9 143429 0.993 4.71 0.445 5 :1@N3_:2@C4 143373 0.992 4.3 0.547 6 :1@N9_:2@C8 143284 0.992 4.32 0.588 7 :1@C4_:2@C5 143228 0.991 4.23 0.469 8 :1@N3_:2@N9 143195 0.991 4.11 0.667 9 :1@N3_:2@C5 143044 0.99 4.53 0.539 10 :1@C4_:2@N7 142993 0.99 4.11 0.556 11 :1@N9_:2@C4 142797 0.988 4.97 0.54 12 :1@N9_:2@N7 142794 0.988 4.4 0.543 13 :1@C4_:2@N3 142784 0.988 4.92 0.598 14 :1@N3_:2@C8 142733 0.988 4.22 0.729 15 :1@C5_:2@N9 142680 0.988 4.49 0.641 16 :1@N1_:2@C4 142679 0.988 4.03 0.743 17 :1@C5_:2@C4 142639 0.987 4.23 0.541 18 :1@N1_:2@N3 142636 0.987 4.14 0.845 19 :1@N3_:2@N7 142568 0.987 4.5 0.659 20 :1@C2_:2@C4 142536 0.987 4.1 0.655 21 :1@N9_:2@C5 142522 0.986 4.79 0.513 22 :1@C6_:2@N3 142513 0.986 4.4 0.758 23 :1@N3_:2@N3 142498 0.986 4.76 0.639 24 :1@C6_:2@C4 142447 0.986 4.11 0.675 25 :1@C5_:2@C8 142426 0.986 4.3 0.687 26 :1@C5_:2@N7 142406 0.986 3.98 0.603 27 :1@C5_:2@C5 142404 0.986 3.9 0.465 28 :1@C6_:2@C5 142191 0.984 3.86 0.576 29 :1@C5_:2@N3 142177 0.984 4.78 0.64 30 :1@N1_:2@C2 142126 0.984 4.24 0.774 31 :1@C2_:2@N3 142077 0.983 4.32 0.75 32 :1@N7_:2@C5 142074 0.983 4.32 0.613 33 :1@C4_:2@C6 142053 0.983 4.84 0.59 34 :1@C6_:2@C2 142029 0.983 4.33 0.709 35 :1@C8_:2@N9 142027 0.983 5.15 0.608 36 :1@C5_:2@C6 141998 0.983 4.19 0.555 37 :1@C2_:2@C5 141988 0.983 4.39 0.629 38 :1@N7_:2@N7 141949 0.983 4.21 0.654 39 :1@N1_:2@C5 141940 0.982 4.1 0.667 40 :1@C8_:2@N7 141933 0.982 4.4 0.673 41 :1@C8_:2@C8 141886 0.982 4.63 0.651 42 :1@C8_:2@C5 141884 0.982 4.78 0.642 43 :1@C6_:2@C6 141873 0.982 3.87 0.498 44 :1@N1_:2@N1 141779 0.981 4.31 0.667 45 :1@C6_:2@N1 141747 0.981 4.09 0.577 46 :1@C6_:2@N9 141706 0.981 4.65 0.776 47 :1@C2_:2@N9 141692 0.981 4.18 0.812 48 :1@N7_:2@C8 141691 0.981 4.67 0.664 49 :1@N7_:2@C4 141670 0.981 4.86 0.678 50 :1@C6_:2@N7 141616 0.98 4.28 0.746 51 :1@O6_:2@N1 141599 0.98 3.91 0.717 52 :1@O6_:2@C5 141597 0.98 4.18 0.673 53 :1@O6_:2@C6 141593 0.98 3.82 0.589 54 :1@C5_:2@N1 141584 0.98 4.67 0.696 55 :1@N3_:2@C6 141565 0.98 5.24 0.619 56 :1@N7_:2@N9 141515 0.98 5.08 0.683 57 :1@C2_:2@C2 141456 0.979 4.75 0.746 58 :1@O6_:2@C4 141447 0.979 4.57 0.799 59 :1@N1_:2@C6 141411 0.979 4.27 0.63 60 :1@N1_:2@N9 141318 0.978 4.46 0.85 61 :1@C5_:2@O6 141263 0.978 4.53 0.629 62 :1@C6_:2@O6 141201 0.977 4.23 0.622 63 :1@N7_:2@C6 141184 0.977 4.51 0.772 64 :1@C8_:2@C4 141175 0.977 5.2 0.666 65 :1@O6_:2@C2 141024 0.976 4.32 0.911 66 :1@C2_:2@N1 140976 0.976 5.01 0.704 67 :1@C5_:2@C2 140969 0.976 4.92 0.695 68 :1@O6_:2@O6 140915 0.975 3.97 0.661 69 :1@C2_:2@C6 140830 0.975 4.89 0.661 70 :1@C4_:2@N1 140820 0.975 5.32 0.735 71 :1@C4_:2@C2 140729 0.974 5.34 0.724 72 :1@C4_:2@O6 140698 0.974 5.36 0.628 73 :1@C6_:2@C8 140560 0.973 4.68 0.778 74 :1@O6_:2@N3 140290 0.971 4.68 0.932 75 :1@N3_:2@C2 140267 0.971 5.32 0.709 76 :1@N9_:2@C6 140083 0.97 5.48 0.697 77 :1@C2_:2@N7 139999 0.969 4.63 0.801 78 :1@N2_:2@C4 139940 0.969 4.54 0.749 79 :1@N3_:2@N1 139852 0.968 5.54 0.706 80 :1@O6_:2@N7 139838 0.968 4.76 0.768 81 :1@C2_:2@C8 139782 0.968 4.48 0.82 82 :1@N1_:2@O6 139488 0.965 4.82 0.782 83 :1@N1_:2@N7 139447 0.965 4.54 0.833 84 :1@N7_:2@O6 139148 0.963 4.59 0.794 85 :1@C6_:2@N2 138838 0.961 4.99 0.813 86 :1@C8_:2@C6 138530 0.959 5.21 0.81 87 :1@N2_:2@N9 138184 0.956 4.53 0.87 88 :1@N2_:2@C5 138162 0.956 5.03 0.692 89 :1@N1_:2@C8 137612 0.953 4.68 0.819 90 :1@N2_:2@N3 137545 0.952 4.48 0.89 91 :1@N7_:2@N1 137243 0.95 5.11 0.913 92 :1@N1_:2@N2 137096 0.949 4.74 0.872 93 :1@N9_:2@N3 136563 0.945 5.67 0.756 94 :1@C2_:2@O6 135574 0.938 5.53 0.803 95 :1@N2_:2@C6 134743 0.933 5.53 0.777 96 :1@N2_:2@C2 134316 0.93 4.96 0.861 97 :1@O6_:2@N2 134057 0.928 4.76 0.964 98 :1@N7_:2@N3 134036 0.928 5.43 0.792 99 :1@N3_:2@O6 133995 0.927 5.85 0.674 100 :1@N2_:2@N1 133811 0.926 5.46 0.812 101 :1@C8_:2@O6 133468 0.924 5.35 0.779 102 :1@O6_:2@C8 133037 0.921 5.29 0.691 103 :1@O6_:2@N9 132500 0.917 5.23 0.701 104 :1@C2_:2@N2 132322 0.916 5.26 0.832 105 :1@N9_:2@O6 132136 0.915 5.83 0.651 106 :1@N2_:2@C8 132030 0.914 4.95 0.781 107 :1@N2_:2@N7 131949 0.913 5.26 0.842 108 :1@N7_:2@C2 129936 0.899 5.45 0.869 109 :1@C5_:2@N2 128847 0.892 5.64 0.712 110 :1@C8_:2@N3 122345 0.847 5.78 0.814 111 :1@N3_:2@N2 119904 0.83 5.89 0.738 112 :1@N2_:2@N2 119389 0.826 5.14 0.87 113 :1@C8_:2@N1 117761 0.815 5.69 0.957 114 :1@N9_:2@N1 116448 0.806 5.88 0.847 115 :1@C4_:2@N2 113244 0.784 5.95 0.733 116 :1@N9_:2@C2 111593 0.772 5.9 0.887 117 :1@C8_:2@C2 102929 0.712 5.82 0.961 118 :1@N2_:2@O6 97902 0.678 5.9 0.937 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 144474, 'v_base2' size 144474, output size 144474 TIME: Analyses took 0.0104 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 144474 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 144474 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 144474 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 144474 COM "COM" (double, distance), size is 144474 v_base1 "v_base1" (vector, vector), size is 144474 v_base2 "v_base2" (vector, vector), size is 144474 normalangle "normalangle" (double), size is 144474 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0010 s ( 0.06%) TIME: Trajectory Process : 1.7542 s ( 99.34%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0104 s ( 0.59%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.7659 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 2.1266 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.