CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:23:50 | Available memory: 7.159 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.c0] Reading '../ctraj.c0' 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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] [vector v_base2 :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] [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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 33424 of 33424) Coordinate processing will occur on 33424 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :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. ----- ctraj.c0 (1-33424, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 108 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@N7' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@O6' Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C4' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@N2' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@O6' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N2' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@O6' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N2' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@O6' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@N2' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@O6' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@N2' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@O6' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@N2' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@O6' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@N2' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C4' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@O6' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@N2' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 33424 frames and processed 33424 frames. TIME: Avg. throughput= 36725.7153 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 101.42 108 # Contact Nframes Frac. Avg Stdev 1 :2@N9_:1@N3 33386 0.999 4.52 0.558 2 :2@N9_:1@C4 33374 0.999 4.63 0.563 3 :2@C4_:1@C4 33312 0.997 4.28 0.519 4 :2@C4_:1@N3 33308 0.997 4.38 0.558 5 :2@N9_:1@C2 33253 0.995 4.82 0.614 6 :2@N9_:1@N9 33236 0.994 4.91 0.678 7 :2@C4_:1@N9 33193 0.993 4.66 0.621 8 :2@N3_:1@N3 33182 0.993 4.53 0.608 9 :2@C4_:1@C2 33161 0.992 4.52 0.689 10 :2@C5_:1@C4 33143 0.992 4.29 0.647 11 :2@C4_:1@C5 33129 0.991 4.4 0.613 12 :2@N3_:1@C4 33103 0.99 4.48 0.605 13 :2@N9_:1@C5 33103 0.99 5.06 0.63 14 :2@N3_:1@C2 33065 0.989 4.35 0.67 15 :2@C5_:1@N3 33055 0.989 4.67 0.697 16 :2@C5_:1@N9 33032 0.988 4.39 0.671 17 :2@N3_:1@C5 33000 0.987 4.37 0.68 18 :2@C4_:1@C6 32981 0.987 4.62 0.619 19 :2@C4_:1@N1 32974 0.987 4.63 0.667 20 :2@N9_:1@N1 32973 0.987 5.22 0.572 21 :2@N3_:1@C6 32967 0.986 4.26 0.624 22 :2@C8_:1@C4 32965 0.986 4.81 0.755 23 :2@N3_:1@N1 32951 0.986 4.22 0.618 24 :2@C8_:1@N3 32937 0.985 4.87 0.717 25 :2@C5_:1@C5 32919 0.985 4.33 0.752 26 :2@C2_:1@N3 32883 0.984 4.92 0.69 27 :2@C6_:1@C4 32873 0.984 4.51 0.643 28 :2@C2_:1@C4 32824 0.982 4.63 0.646 29 :2@C2_:1@C5 32811 0.982 4.2 0.68 30 :2@N1_:1@C4 32801 0.981 4.7 0.616 31 :2@C2_:1@C6 32785 0.981 4.01 0.68 32 :2@N9_:1@C6 32771 0.98 5.38 0.573 33 :2@C6_:1@N9 32734 0.979 4.64 0.631 34 :2@C4_:1@N7 32734 0.979 4.85 0.774 35 :2@N1_:1@C5 32723 0.979 4.16 0.672 36 :2@C2_:1@C2 32718 0.979 4.67 0.788 37 :2@N7_:1@C4 32687 0.978 4.63 0.822 38 :2@C6_:1@C5 32676 0.978 4.18 0.761 39 :2@C2_:1@N1 32667 0.977 4.24 0.764 40 :2@N3_:1@O6 32644 0.977 4.66 0.727 41 :2@C4_:1@C8 32613 0.976 4.93 0.769 42 :2@N1_:1@N3 32613 0.976 5.22 0.738 43 :2@C6_:1@N3 32612 0.976 5.08 0.752 44 :2@C5_:1@N7 32602 0.975 4.47 0.852 45 :2@N3_:1@N2 32601 0.975 4.84 0.874 46 :2@C5_:1@C8 32562 0.974 4.45 0.834 47 :2@C4_:1@N2 32541 0.974 5.06 0.854 48 :2@N7_:1@N3 32500 0.972 4.97 0.787 49 :2@C2_:1@O6 32496 0.972 4.15 0.789 50 :2@N1_:1@C6 32451 0.971 4.15 0.809 51 :2@C6_:1@N7 32446 0.971 4.12 0.85 52 :2@N3_:1@N9 32374 0.969 5.06 0.728 53 :2@N1_:1@N7 32328 0.967 4.23 0.813 54 :2@C8_:1@N9 32317 0.967 4.72 0.804 55 :2@C6_:1@C8 32299 0.966 4.36 0.797 56 :2@C5_:1@C2 32228 0.964 4.95 0.844 57 :2@N7_:1@N9 32214 0.964 4.42 0.824 58 :2@C4_:1@O6 32194 0.963 5.19 0.655 59 :2@N1_:1@N9 32081 0.96 5.03 0.667 60 :2@C8_:1@C2 32071 0.96 5.38 0.736 61 :2@C2_:1@N7 32057 0.959 4.56 0.873 62 :2@N6_:1@C4 31935 0.955 5.02 0.738 63 :2@C5_:1@C6 31916 0.955 4.72 0.761 64 :2@N3_:1@N7 31915 0.955 4.89 0.836 65 :2@N6_:1@N9 31909 0.955 4.93 0.684 66 :2@C8_:1@C5 31843 0.953 5.27 0.733 67 :2@N9_:1@C8 31736 0.949 5.38 0.758 68 :2@N1_:1@O6 31695 0.948 4.19 0.84 69 :2@N1_:1@C8 31645 0.947 4.7 0.802 70 :2@N1_:1@N1 31640 0.947 4.59 0.908 71 :2@C2_:1@N9 31620 0.946 5.15 0.768 72 :2@C6_:1@C6 31592 0.945 4.43 0.834 73 :2@N1_:1@C2 31526 0.943 5.07 0.893 74 :2@N6_:1@N7 31504 0.943 4.18 0.938 75 :2@N6_:1@C8 31466 0.941 4.38 0.83 76 :2@N7_:1@C8 31456 0.941 4.6 0.942 77 :2@N7_:1@C5 31437 0.941 4.87 0.816 78 :2@N9_:1@N7 31427 0.94 5.5 0.735 79 :2@N6_:1@C5 31322 0.937 4.53 0.839 80 :2@C5_:1@N1 31178 0.933 4.94 0.811 81 :2@C8_:1@C8 31173 0.933 5.17 0.86 82 :2@N3_:1@C8 30948 0.926 5.18 0.805 83 :2@C2_:1@C8 30916 0.925 5.02 0.879 84 :2@C2_:1@N2 30666 0.917 5.22 0.913 85 :2@N7_:1@N7 30633 0.916 4.89 0.884 86 :2@C6_:1@C2 30624 0.916 5.14 0.9 87 :2@C6_:1@N1 30331 0.907 4.85 0.899 88 :2@C6_:1@O6 30140 0.902 4.64 0.771 89 :2@N7_:1@C2 29943 0.896 5.39 0.798 90 :2@C5_:1@O6 29840 0.893 5.16 0.659 91 :2@C8_:1@N7 29678 0.888 5.45 0.764 92 :2@C8_:1@N1 29493 0.882 5.73 0.65 93 :2@C8_:1@C6 29317 0.877 5.74 0.608 94 :2@N9_:1@O6 29311 0.877 6 0.548 95 :2@N6_:1@C6 29299 0.877 4.82 0.855 96 :2@N7_:1@C6 29152 0.872 5.41 0.703 97 :2@C8_:1@N2 29053 0.869 5.75 0.779 98 :2@N6_:1@N3 28880 0.864 5.64 0.761 99 :2@N7_:1@N1 28461 0.852 5.59 0.769 100 :2@N6_:1@O6 28399 0.85 4.94 0.884 101 :2@C5_:1@N2 28301 0.847 5.48 0.868 102 :2@N6_:1@N1 26772 0.801 5.37 0.931 103 :2@N7_:1@O6 25825 0.773 5.96 0.665 104 :2@N1_:1@N2 25208 0.754 5.51 0.902 105 :2@N6_:1@C2 24572 0.735 5.6 0.874 106 :2@N7_:1@N2 24338 0.728 5.82 0.823 107 :2@C6_:1@N2 23765 0.711 5.58 0.905 108 :2@N6_:1@N2 14817 0.443 5.79 1.02 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 33424, 'v_base2' size 33424, output size 33424 TIME: Analyses took 0.0059 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 33424 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 33424 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 33424 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 33424 COM "COM" (double, distance), size is 33424 v_base1 "v_base1" (vector, vector), size is 33424 v_base2 "v_base2" (vector, vector), size is 33424 normalangle "normalangle" (double), size is 33424 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.9101 s ( 99.30%) TIME: Action Post : 0.0004 s ( 0.04%) TIME: Analysis : 0.0059 s ( 0.64%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.9165 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: 1.0883 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.