CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 16:15:30 | Available memory: 887.961 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.c3] Reading '../ctraj.c3' 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_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: 0: noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 101615 of 101615) Coordinate processing will occur on 101615 frames. TIME: Run Initialization took 0.0025 seconds. 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.c3 (1-101615, 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 121 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@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 101615 frames and processed 101615 frames. TIME: Trajectory processing: 1.7291 s TIME: Avg. throughput= 58768.3147 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 108.447 121 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 101299 0.997 4.31 0.554 2 :1@N3_:2@C6 101264 0.997 4.07 0.554 3 :1@N3_:2@C5 101262 0.997 4.31 0.494 4 :1@N3_:2@O6 101170 0.996 4.29 0.671 5 :1@N3_:2@C4 101081 0.995 4.67 0.549 6 :1@C2_:2@C6 101063 0.995 4.12 0.588 7 :1@C2_:2@O6 100993 0.994 4.09 0.702 8 :1@N1_:2@O6 100992 0.994 3.9 0.732 9 :1@C4_:2@N7 100886 0.993 4.74 0.635 10 :1@N1_:2@C6 100856 0.993 4.23 0.677 11 :1@N9_:2@N9 100808 0.992 5.32 0.539 12 :1@N9_:2@C5 100795 0.992 4.54 0.653 13 :1@C4_:2@C4 100715 0.991 4.77 0.574 14 :1@C2_:2@C5 100707 0.991 4.64 0.658 15 :1@N3_:2@N7 100685 0.991 4.81 0.738 16 :1@C2_:2@N1 100664 0.991 4.18 0.823 17 :1@N3_:2@N1 100481 0.989 4.16 0.75 18 :1@C4_:2@C6 100368 0.988 4.02 0.636 19 :1@C4_:2@O6 100324 0.987 4.16 0.698 20 :1@N2_:2@C6 100275 0.987 4.62 0.732 21 :1@C4_:2@N9 100274 0.987 5.44 0.546 22 :1@N9_:2@N7 100261 0.987 4.81 0.757 23 :1@N3_:2@N3 100079 0.985 4.82 0.675 24 :1@N1_:2@C5 100065 0.985 5.01 0.714 25 :1@N3_:2@N9 100018 0.984 5.34 0.661 26 :1@C2_:2@C4 99814 0.982 5.16 0.672 27 :1@N2_:2@O6 99409 0.978 4.62 0.873 28 :1@N2_:2@N1 99392 0.978 4.54 0.961 29 :1@C6_:2@O6 99253 0.977 3.78 0.757 30 :1@C4_:2@C8 99047 0.975 5.32 0.623 31 :1@N3_:2@C8 98994 0.974 5.33 0.797 32 :1@C5_:2@C5 98914 0.973 4.64 0.666 33 :1@N9_:2@C8 98895 0.973 5.2 0.68 34 :1@N2_:2@C5 98520 0.97 5.08 0.832 35 :1@N9_:2@C4 98430 0.969 4.79 0.53 36 :1@N3_:2@C2 98410 0.968 4.48 0.717 37 :1@C5_:2@O6 98172 0.966 3.87 0.714 38 :1@C5_:2@N7 98007 0.964 5.04 0.73 39 :1@C6_:2@C6 97842 0.963 4.19 0.631 40 :1@C2_:2@N7 97815 0.963 5.15 0.95 41 :1@C2_:2@C2 97785 0.962 4.68 0.856 42 :1@N9_:2@C6 97715 0.962 4.48 0.612 43 :1@N1_:2@N1 97648 0.961 4.27 0.699 44 :1@C5_:2@C6 97544 0.96 4.03 0.599 45 :1@N9_:2@O6 97490 0.959 4.77 0.682 46 :1@C6_:2@C5 97460 0.959 5.02 0.678 47 :1@C4_:2@N1 97323 0.958 4.14 0.616 48 :1@C2_:2@N3 97103 0.956 5.22 0.748 49 :1@C4_:2@N3 96864 0.953 4.93 0.557 50 :1@C4_:2@C2 96654 0.951 4.59 0.643 51 :1@C5_:2@N1 96542 0.95 4.27 0.708 52 :1@C6_:2@N1 96508 0.95 4.37 0.636 53 :1@O6_:2@O6 96138 0.946 4.08 0.722 54 :1@C5_:2@C4 96077 0.946 5.28 0.56 55 :1@C8_:2@C5 96009 0.945 4.88 0.709 56 :1@C8_:2@C6 96007 0.945 4.75 0.712 57 :1@N7_:2@C6 95990 0.945 4.56 0.726 58 :1@N9_:2@N3 95885 0.944 5.01 0.682 59 :1@N7_:2@O6 95599 0.941 4.37 0.808 60 :1@N9_:2@N1 95518 0.94 4.64 0.722 61 :1@N1_:2@C2 95354 0.938 5.06 0.738 62 :1@C8_:2@C4 95303 0.938 5.33 0.635 63 :1@O6_:2@C6 95246 0.937 4.74 0.641 64 :1@C8_:2@O6 95240 0.937 4.84 0.779 65 :1@O6_:2@N1 95177 0.937 4.97 0.713 66 :1@N3_:2@N2 95076 0.936 4.96 0.824 67 :1@C6_:2@N7 95001 0.935 5.48 0.743 68 :1@C5_:2@C2 94976 0.935 4.97 0.755 69 :1@N2_:2@C4 94835 0.933 5.44 0.756 70 :1@N7_:2@C5 94820 0.933 4.97 0.672 71 :1@C6_:2@C2 94545 0.93 5.26 0.662 72 :1@C5_:2@N3 94526 0.93 5.5 0.639 73 :1@N2_:2@C2 94359 0.929 4.86 1.07 74 :1@N1_:2@C4 94215 0.927 5.66 0.654 75 :1@N9_:2@C2 94136 0.926 4.85 0.807 76 :1@N1_:2@N7 93794 0.923 5.46 0.872 77 :1@N7_:2@N1 93548 0.921 4.79 0.934 78 :1@N7_:2@C4 93431 0.919 5.64 0.617 79 :1@C8_:2@N7 92822 0.913 4.99 0.94 80 :1@C4_:2@N2 92730 0.913 5.12 0.738 81 :1@C8_:2@N1 92064 0.906 4.92 0.891 82 :1@C5_:2@C8 91887 0.904 5.78 0.636 83 :1@C6_:2@C4 91880 0.904 5.76 0.577 84 :1@C2_:2@N2 91461 0.9 4.98 1.01 85 :1@C8_:2@N9 91168 0.897 5.8 0.607 86 :1@N1_:2@N3 90686 0.892 5.73 0.639 87 :1@O6_:2@C5 90551 0.891 5.65 0.628 88 :1@N2_:2@N3 90527 0.891 5.35 0.85 89 :1@N7_:2@N7 90053 0.886 5.15 0.852 90 :1@C5_:2@N9 89769 0.883 6.02 0.539 91 :1@N1_:2@N2 89618 0.882 5.39 0.881 92 :1@C8_:2@N3 89057 0.876 5.5 0.85 93 :1@C2_:2@N9 88986 0.876 5.83 0.742 94 :1@C6_:2@N3 88877 0.875 5.92 0.567 95 :1@C8_:2@C2 87446 0.861 5.2 1.05 96 :1@C8_:2@C8 87153 0.858 5.45 0.778 97 :1@N7_:2@C2 86983 0.856 5.31 1.02 98 :1@C6_:2@N2 86849 0.855 5.63 0.727 99 :1@C5_:2@N2 86768 0.854 5.37 0.864 100 :1@C2_:2@C8 85763 0.844 5.69 0.933 101 :1@N9_:2@N2 85588 0.842 5.28 0.975 102 :1@O6_:2@C2 84288 0.829 5.85 0.642 103 :1@N2_:2@N7 84073 0.827 5.33 1.18 104 :1@N7_:2@N3 83764 0.824 5.77 0.791 105 :1@N7_:2@N9 79992 0.787 6.18 0.544 106 :1@O6_:2@N7 79376 0.781 5.98 0.716 107 :1@N7_:2@C8 78728 0.775 5.76 0.657 108 :1@N2_:2@N2 76694 0.755 4.6 1.16 109 :1@C6_:2@C8 72609 0.715 6.19 0.65 110 :1@N2_:2@N9 71235 0.701 5.86 0.836 111 :1@O6_:2@N2 67946 0.669 6 0.688 112 :1@N1_:2@C8 67761 0.667 6.01 0.812 113 :1@O6_:2@C4 65832 0.648 6.32 0.496 114 :1@N1_:2@N9 64535 0.635 6.22 0.645 115 :1@C8_:2@N2 63557 0.625 5.07 1.27 116 :1@N7_:2@N2 62237 0.612 5.16 1.17 117 :1@N2_:2@C8 61512 0.605 5.53 1.1 118 :1@C6_:2@N9 59298 0.584 6.34 0.532 119 :1@O6_:2@N3 54728 0.539 6.37 0.471 120 :1@O6_:2@C8 29269 0.288 6.31 0.585 121 :1@O6_:2@N9 17941 0.177 6.48 0.4 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0145 seconds. DATASETS: 9 data sets: [traj] "[traj]" (topology), size is 67 noWAt.topo.hmr, 67 atoms, 2 res, box: Orthogonal, 1 mol RMSD_00001 "RMSD_00001" (double, rms), size is 101615 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 101615 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 101615 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 101615 COM "COM" (double, distance), size is 101615 v_base1 "v_base1" (vector, vector), size is 101615 v_base2 "v_base2" (vector, vector), size is 101615 normalangle "normalangle" (double), size is 101615 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' Warning: 'Contacts_00001[mindist]' selects no data sets. Warning: Contacts_00001[mindist] does not correspond to any data sets. COM normalangle TIME: Total execution time: 2.0170 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.