CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 14:44:20 | Available memory: 1.617 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.c1] Reading '../ctraj.c1' 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,C2,N3,C4,C5,C6,N6,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,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :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,N6,H61,H62,N7,C8,H8,N9 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,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,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, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 123549 of 123549) Coordinate processing will occur on 123549 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*](42) Reference mask: [:1,2&!@H*](42) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :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,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] 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,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c1 (1-123549, 1) ----- 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 107 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@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@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@O6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N2' Atom ':1@N6' to ':2@N3' 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@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@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@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@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 123549 frames and processed 123549 frames. TIME: Avg. throughput= 80276.5095 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 100.072 107 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 122093 0.988 4.48 0.581 2 :1@C2_:2@N9 121269 0.982 4.67 0.649 3 :1@N3_:2@C4 120749 0.977 4.44 0.6 4 :1@C4_:2@N9 120742 0.977 4.57 0.51 5 :1@N3_:2@N3 120470 0.975 4.72 0.604 6 :1@C4_:2@C4 119910 0.971 4.28 0.509 7 :1@N9_:2@N9 119896 0.97 4.94 0.564 8 :1@C2_:2@C4 119845 0.97 4.5 0.712 9 :1@C4_:2@N3 119829 0.97 4.61 0.603 10 :1@C2_:2@N3 119765 0.969 4.45 0.672 11 :1@N1_:2@N9 119726 0.969 5 0.6 12 :1@N9_:2@C4 119469 0.967 4.71 0.586 13 :1@N3_:2@C8 119388 0.966 4.72 0.7 14 :1@N1_:2@N3 119055 0.964 4.18 0.599 15 :1@C5_:2@N9 119009 0.963 4.9 0.554 16 :1@C6_:2@N3 118830 0.962 4.1 0.561 17 :1@C5_:2@N3 118830 0.962 4.33 0.663 18 :1@C5_:2@C4 118798 0.962 4.26 0.564 19 :1@C4_:2@C8 118643 0.96 4.64 0.634 20 :1@N1_:2@C4 118580 0.96 4.52 0.663 21 :1@C6_:2@N9 118498 0.959 5.1 0.543 22 :1@N9_:2@C5 118476 0.959 4.3 0.546 23 :1@N9_:2@C8 118460 0.959 4.67 0.646 24 :1@C6_:2@C4 118391 0.958 4.39 0.566 25 :1@C4_:2@C5 118326 0.958 4.2 0.535 26 :1@C4_:2@C2 118133 0.956 4.79 0.627 27 :1@N3_:2@C2 118097 0.956 5.17 0.627 28 :1@N3_:2@C5 118070 0.956 4.67 0.641 29 :1@C5_:2@C2 117955 0.955 4.2 0.679 30 :1@N9_:2@N3 117939 0.955 5.26 0.711 31 :1@C6_:2@C2 117823 0.954 3.96 0.592 32 :1@C8_:2@C4 117748 0.953 4.89 0.749 33 :1@N9_:2@N7 117721 0.953 4.29 0.647 34 :1@N6_:2@N3 117700 0.953 4.38 0.639 35 :1@N7_:2@C4 117629 0.952 4.7 0.748 36 :1@C6_:2@N2 117501 0.951 4.22 0.703 37 :1@C5_:2@C5 117500 0.951 4.14 0.609 38 :1@N9_:2@C6 117497 0.951 4.55 0.562 39 :1@C4_:2@N1 117428 0.95 4.77 0.565 40 :1@C2_:2@C8 117382 0.95 5.2 0.75 41 :1@C8_:2@C5 117364 0.95 4.27 0.706 42 :1@C2_:2@C2 117331 0.95 4.87 0.709 43 :1@C4_:2@C6 117306 0.949 4.5 0.535 44 :1@N1_:2@C2 117237 0.949 4.33 0.682 45 :1@C4_:2@N7 117149 0.948 4.44 0.669 46 :1@C5_:2@N1 117023 0.947 4.08 0.579 47 :1@N3_:2@N7 117011 0.947 4.85 0.727 48 :1@C8_:2@N9 116990 0.947 5.41 0.689 49 :1@N1_:2@N2 116815 0.945 4.55 0.694 50 :1@N7_:2@C5 116776 0.945 4.21 0.696 51 :1@N6_:2@C2 116767 0.945 3.93 0.649 52 :1@N6_:2@N2 116761 0.945 3.86 0.776 53 :1@C8_:2@C6 116718 0.945 4.12 0.699 54 :1@C5_:2@C6 116653 0.944 4.06 0.589 55 :1@N7_:2@N3 116629 0.944 4.86 0.882 56 :1@N7_:2@N1 116476 0.943 4 0.788 57 :1@N7_:2@C6 116408 0.942 3.83 0.657 58 :1@N3_:2@C6 116384 0.942 5.23 0.64 59 :1@C5_:2@N2 116318 0.941 4.73 0.809 60 :1@N3_:2@N1 116290 0.941 5.41 0.625 61 :1@N9_:2@N1 116287 0.941 5.08 0.677 62 :1@C2_:2@C5 116283 0.941 4.97 0.783 63 :1@N7_:2@C2 116253 0.941 4.48 0.928 64 :1@C8_:2@N7 116186 0.94 4.45 0.755 65 :1@N9_:2@O6 116179 0.94 4.79 0.567 66 :1@C5_:2@C8 116096 0.94 5.09 0.633 67 :1@C6_:2@N1 115988 0.939 4.14 0.635 68 :1@C8_:2@O6 115987 0.939 4.12 0.656 69 :1@N6_:2@C4 115940 0.938 4.92 0.592 70 :1@N7_:2@N9 115876 0.938 5.43 0.676 71 :1@C2_:2@N2 115803 0.937 5.31 0.709 72 :1@C8_:2@N1 115599 0.936 4.6 0.84 73 :1@C8_:2@C8 115505 0.935 5.11 0.715 74 :1@C6_:2@C5 115497 0.935 4.56 0.69 75 :1@C4_:2@O6 115212 0.933 4.98 0.577 76 :1@C5_:2@N7 115168 0.932 4.69 0.704 77 :1@N7_:2@O6 115065 0.931 3.9 0.612 78 :1@N1_:2@C5 114869 0.93 4.96 0.797 79 :1@N1_:2@N1 114657 0.928 4.79 0.778 80 :1@C6_:2@C6 114430 0.926 4.44 0.727 81 :1@C2_:2@N1 114342 0.925 5.33 0.746 82 :1@N9_:2@C2 114293 0.925 5.34 0.738 83 :1@N6_:2@N1 114251 0.925 4.07 0.664 84 :1@N7_:2@N7 114234 0.925 4.71 0.724 85 :1@C5_:2@O6 114138 0.924 4.45 0.624 86 :1@C2_:2@N7 114060 0.923 5.4 0.817 87 :1@N1_:2@C6 113529 0.919 5.14 0.859 88 :1@C2_:2@C6 113462 0.918 5.42 0.791 89 :1@N1_:2@C8 113049 0.915 5.61 0.708 90 :1@C4_:2@N2 113032 0.915 5.44 0.7 91 :1@N7_:2@C8 112825 0.913 5.37 0.667 92 :1@N6_:2@C6 112766 0.913 4.67 0.806 93 :1@C6_:2@C8 112637 0.912 5.55 0.637 94 :1@N6_:2@C5 112636 0.912 5.06 0.714 95 :1@C6_:2@O6 112301 0.909 5.04 0.859 96 :1@C6_:2@N7 112201 0.908 5.31 0.767 97 :1@N3_:2@N2 112038 0.907 5.78 0.644 98 :1@N6_:2@N9 111766 0.905 5.78 0.539 99 :1@C8_:2@N3 111743 0.904 5.27 0.816 100 :1@C8_:2@C2 111135 0.9 5.06 0.874 101 :1@N1_:2@N7 109830 0.889 5.63 0.825 102 :1@N6_:2@O6 109250 0.884 5.16 0.976 103 :1@N7_:2@N2 108260 0.876 4.93 0.956 104 :1@N6_:2@N7 97832 0.792 5.87 0.727 105 :1@C8_:2@N2 92756 0.751 5.53 0.836 106 :1@N9_:2@N2 92439 0.748 5.88 0.738 107 :1@N6_:2@C8 90567 0.733 6.16 0.561 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 123549, 'v_base2' size 123549, output size 123549 TIME: Analyses took 0.0108 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 123549 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 123549 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 123549 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 123549 COM "COM" (double, distance), size is 123549 v_base1 "v_base1" (vector, vector), size is 123549 v_base2 "v_base2" (vector, vector), size is 123549 normalangle "normalangle" (double), size is 123549 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.13%) TIME: Trajectory Process : 1.5390 s ( 99.15%) TIME: Action Post : 0.0002 s ( 0.02%) TIME: Analysis : 0.0108 s ( 0.70%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.5522 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: 1.8875 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.