CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:32:35 | Available memory: 1.221 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,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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 143536 of 143536) Coordinate processing will occur on 143536 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.c1 (1-143536, 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 143536 frames and processed 143536 frames. TIME: Avg. throughput= 82938.2476 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 110.263 118 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 140520 0.979 4.1 0.673 2 :1@C4_:2@N9 140329 0.978 4.31 0.659 3 :1@N3_:2@C8 140286 0.977 4.25 0.723 4 :1@C4_:2@C8 140274 0.977 4.19 0.794 5 :1@N3_:2@C4 140004 0.975 4.27 0.537 6 :1@N3_:2@N7 139624 0.973 4.52 0.646 7 :1@N9_:2@N9 139479 0.972 4.8 0.524 8 :1@C4_:2@C4 139428 0.971 4.31 0.497 9 :1@C2_:2@N9 139366 0.971 4.18 0.819 10 :1@N9_:2@C8 139290 0.97 4.47 0.778 11 :1@C2_:2@C4 139201 0.97 4.1 0.665 12 :1@N3_:2@C5 139181 0.97 4.5 0.565 13 :1@C4_:2@C5 139094 0.969 4.24 0.48 14 :1@C4_:2@N7 138989 0.968 4.19 0.62 15 :1@N3_:2@N3 138868 0.967 4.71 0.558 16 :1@N9_:2@C4 138756 0.967 4.96 0.545 17 :1@N9_:2@N7 138686 0.966 4.51 0.677 18 :1@C4_:2@N3 138559 0.965 4.88 0.596 19 :1@N9_:2@C5 138551 0.965 4.81 0.51 20 :1@C2_:2@N3 138540 0.965 4.32 0.746 21 :1@N1_:2@C4 138362 0.964 4.07 0.806 22 :1@C5_:2@C4 138288 0.963 4.3 0.591 23 :1@C5_:2@N7 138228 0.963 4.09 0.759 24 :1@C5_:2@C5 138226 0.963 3.96 0.539 25 :1@C5_:2@N9 138027 0.962 4.62 0.756 26 :1@N2_:2@C4 137967 0.961 4.51 0.725 27 :1@C2_:2@C8 137964 0.961 4.48 0.785 28 :1@N1_:2@N9 137956 0.961 4.52 0.926 29 :1@N1_:2@N3 137936 0.961 4.18 0.94 30 :1@C2_:2@C5 137921 0.961 4.37 0.618 31 :1@C6_:2@C5 137914 0.961 3.93 0.628 32 :1@C6_:2@C4 137909 0.961 4.21 0.761 33 :1@C4_:2@C6 137890 0.961 4.79 0.623 34 :1@C6_:2@N3 137865 0.96 4.48 0.821 35 :1@C8_:2@C5 137775 0.96 4.83 0.669 36 :1@C5_:2@C6 137768 0.96 4.16 0.554 37 :1@N1_:2@C5 137726 0.96 4.13 0.643 38 :1@N7_:2@C5 137720 0.959 4.4 0.697 39 :1@C5_:2@N3 137705 0.959 4.81 0.624 40 :1@C6_:2@C6 137531 0.958 3.88 0.508 41 :1@N1_:2@C2 137501 0.958 4.29 0.822 42 :1@C6_:2@N7 137486 0.958 4.36 0.797 43 :1@C6_:2@C2 137445 0.958 4.37 0.727 44 :1@C2_:2@C2 137383 0.957 4.75 0.685 45 :1@N3_:2@C6 137359 0.957 5.18 0.698 46 :1@N7_:2@C4 137341 0.957 4.96 0.675 47 :1@N1_:2@N1 137330 0.957 4.35 0.663 48 :1@N2_:2@N9 137303 0.957 4.48 0.81 49 :1@C6_:2@N1 137201 0.956 4.1 0.576 50 :1@C5_:2@N1 137186 0.956 4.59 0.732 51 :1@N1_:2@C6 137140 0.955 4.29 0.62 52 :1@C5_:2@C8 137111 0.955 4.43 0.842 53 :1@C5_:2@O6 137100 0.955 4.48 0.614 54 :1@C8_:2@C4 137082 0.955 5.26 0.654 55 :1@O6_:2@C6 137076 0.955 3.86 0.614 56 :1@O6_:2@C5 137056 0.955 4.28 0.752 57 :1@O6_:2@N1 137049 0.955 3.97 0.732 58 :1@N3_:2@C2 137011 0.955 5.25 0.656 59 :1@C6_:2@O6 136964 0.954 4.2 0.646 60 :1@N7_:2@C6 136952 0.954 4.48 0.74 61 :1@C2_:2@N7 136812 0.953 4.62 0.752 62 :1@C2_:2@N1 136723 0.953 5 0.678 63 :1@N2_:2@N3 136697 0.952 4.52 0.906 64 :1@C4_:2@N1 136643 0.952 5.21 0.815 65 :1@C4_:2@O6 136615 0.952 5.3 0.672 66 :1@C4_:2@C2 136591 0.952 5.23 0.773 67 :1@C2_:2@C6 136588 0.952 4.87 0.699 68 :1@C5_:2@C2 136576 0.952 4.87 0.71 69 :1@O6_:2@O6 136487 0.951 3.95 0.653 70 :1@O6_:2@C2 136429 0.95 4.43 0.947 71 :1@N9_:2@C6 136305 0.95 5.41 0.702 72 :1@C8_:2@N9 136024 0.948 5.29 0.624 73 :1@N7_:2@O6 135823 0.946 4.54 0.71 74 :1@N3_:2@N1 135817 0.946 5.46 0.74 75 :1@O6_:2@C4 135743 0.946 4.7 0.873 76 :1@N1_:2@N7 135742 0.946 4.57 0.773 77 :1@N2_:2@C5 135559 0.944 4.99 0.719 78 :1@N1_:2@C8 135404 0.943 4.74 0.834 79 :1@C6_:2@N9 135358 0.943 4.74 0.855 80 :1@N1_:2@O6 135264 0.942 4.8 0.821 81 :1@C6_:2@C8 135110 0.941 4.77 0.849 82 :1@C8_:2@C6 135040 0.941 5.16 0.775 83 :1@C8_:2@N7 134965 0.94 4.49 0.823 84 :1@N7_:2@N7 134914 0.94 4.3 0.838 85 :1@O6_:2@N7 134474 0.937 4.83 0.832 86 :1@C6_:2@N2 134443 0.937 5.02 0.82 87 :1@O6_:2@N3 134280 0.936 4.81 0.98 88 :1@C8_:2@O6 133581 0.931 5.34 0.735 89 :1@N7_:2@N1 133274 0.929 4.99 0.953 90 :1@N2_:2@C8 133017 0.927 4.91 0.756 91 :1@N2_:2@C2 132708 0.925 5.03 0.824 92 :1@N7_:2@N9 132688 0.924 5.22 0.672 93 :1@N9_:2@N3 132666 0.924 5.57 0.829 94 :1@N1_:2@N2 132057 0.92 4.79 0.899 95 :1@C8_:2@C8 131766 0.918 4.72 0.766 96 :1@C2_:2@N2 131766 0.918 5.32 0.772 97 :1@C2_:2@O6 131360 0.915 5.5 0.888 98 :1@N2_:2@N7 131243 0.914 5.21 0.863 99 :1@N2_:2@C6 130870 0.912 5.51 0.811 100 :1@N7_:2@N3 130496 0.909 5.47 0.731 101 :1@N9_:2@O6 130459 0.909 5.78 0.638 102 :1@N2_:2@N1 130068 0.906 5.49 0.758 103 :1@N3_:2@O6 129807 0.904 5.79 0.787 104 :1@N7_:2@C8 129748 0.904 4.73 0.739 105 :1@O6_:2@N2 129491 0.902 4.87 0.993 106 :1@N7_:2@C2 126406 0.881 5.37 0.915 107 :1@C5_:2@N2 125204 0.872 5.54 0.774 108 :1@N3_:2@N2 123523 0.861 5.89 0.685 109 :1@O6_:2@C8 122890 0.856 5.31 0.704 110 :1@O6_:2@N9 121537 0.847 5.26 0.693 111 :1@C8_:2@N3 118953 0.829 5.72 0.848 112 :1@N2_:2@N2 117968 0.822 5.27 0.834 113 :1@C8_:2@N1 115694 0.806 5.51 1.03 114 :1@N9_:2@N1 114748 0.799 5.7 0.961 115 :1@C4_:2@N2 112873 0.786 5.81 0.819 116 :1@N9_:2@C2 109261 0.761 5.69 1.03 117 :1@C8_:2@C2 100282 0.699 5.6 1.09 118 :1@N2_:2@O6 94119 0.656 5.87 1 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 143536, 'v_base2' size 143536, output size 143536 TIME: Analyses took 0.0105 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 143536 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 143536 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 143536 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 143536 COM "COM" (double, distance), size is 143536 v_base1 "v_base1" (vector, vector), size is 143536 v_base2 "v_base2" (vector, vector), size is 143536 normalangle "normalangle" (double), size is 143536 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0009 s ( 0.05%) TIME: Trajectory Process : 1.7306 s ( 99.33%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0105 s ( 0.60%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.7423 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: 2.0966 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.