CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 16:14:55 | Available memory: 1179.69 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.c0] Reading '../ctraj.c0' 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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 135545 of 135545) Coordinate processing will occur on 135545 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.c0 (1-135545, 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 119 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@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 135545 frames and processed 135545 frames. TIME: Trajectory processing: 2.4047 s TIME: Avg. throughput= 56365.8078 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 112.878 119 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 135464 0.999 4.23 0.51 2 :1@C4_:2@C5 135461 0.999 4.26 0.59 3 :1@N3_:2@C4 135345 0.999 4.42 0.56 4 :1@N9_:2@C5 135265 0.998 4.24 0.563 5 :1@C4_:2@C6 135246 0.998 4.55 0.621 6 :1@C4_:2@N9 135164 0.997 4.56 0.549 7 :1@N3_:2@N9 135122 0.997 4.51 0.522 8 :1@C5_:2@C5 135076 0.997 4.28 0.733 9 :1@N3_:2@N3 135048 0.996 4.58 0.598 10 :1@N9_:2@N9 135048 0.996 4.79 0.642 11 :1@N9_:2@N7 135018 0.996 4.3 0.717 12 :1@C5_:2@C4 135018 0.996 4.33 0.63 13 :1@N3_:2@C5 135017 0.996 4.77 0.674 14 :1@N9_:2@C4 135016 0.996 4.55 0.601 15 :1@C4_:2@N3 134897 0.995 4.47 0.588 16 :1@C5_:2@C6 134879 0.995 4.18 0.745 17 :1@N9_:2@C8 134868 0.995 4.62 0.736 18 :1@C2_:2@C4 134857 0.995 4.62 0.676 19 :1@C5_:2@N1 134854 0.995 4.11 0.66 20 :1@N1_:2@N3 134838 0.995 4.27 0.638 21 :1@C6_:2@C2 134827 0.995 4.02 0.695 22 :1@C2_:2@N3 134800 0.995 4.43 0.669 23 :1@N9_:2@C6 134753 0.994 4.52 0.562 24 :1@C4_:2@N1 134730 0.994 4.71 0.604 25 :1@C4_:2@C8 134588 0.993 4.74 0.688 26 :1@C8_:2@C5 134577 0.993 4.22 0.772 27 :1@C4_:2@N7 134569 0.993 4.6 0.745 28 :1@N1_:2@C4 134507 0.992 4.72 0.677 29 :1@N1_:2@C2 134498 0.992 4.35 0.785 30 :1@C6_:2@N3 134429 0.992 4.23 0.631 31 :1@N3_:2@C8 134411 0.992 4.89 0.663 32 :1@N7_:2@C6 134363 0.991 3.92 0.792 33 :1@N9_:2@O6 134315 0.991 4.84 0.609 34 :1@C6_:2@C4 134255 0.99 4.62 0.637 35 :1@C2_:2@N9 134253 0.99 4.85 0.576 36 :1@C5_:2@N3 134227 0.99 4.3 0.673 37 :1@C5_:2@C2 134215 0.99 4.16 0.663 38 :1@N7_:2@C5 134080 0.989 4.27 0.822 39 :1@N3_:2@C2 134016 0.989 5.02 0.672 40 :1@C8_:2@C6 133961 0.988 4.11 0.708 41 :1@C4_:2@C2 133949 0.988 4.65 0.6 42 :1@C8_:2@O6 133915 0.988 4.19 0.726 43 :1@C2_:2@C2 133911 0.988 4.81 0.793 44 :1@N1_:2@N2 133688 0.986 4.46 0.807 45 :1@C6_:2@N1 133583 0.986 4.21 0.801 46 :1@O6_:2@C2 133512 0.985 4.11 0.787 47 :1@C6_:2@N2 133440 0.984 4.14 0.733 48 :1@N3_:2@N7 133371 0.984 5.05 0.732 49 :1@C5_:2@N9 133287 0.983 4.98 0.616 50 :1@C8_:2@N7 133274 0.983 4.43 0.882 51 :1@N3_:2@N1 133222 0.983 5.34 0.72 52 :1@N7_:2@N1 133216 0.983 4.02 0.761 53 :1@N3_:2@C6 133143 0.982 5.27 0.724 54 :1@N1_:2@N9 132755 0.979 5.25 0.562 55 :1@C8_:2@C4 132721 0.979 4.75 0.755 56 :1@N2_:2@N3 132532 0.978 4.95 0.867 57 :1@N7_:2@C4 132459 0.977 4.67 0.766 58 :1@N2_:2@N9 132393 0.977 5.28 0.691 59 :1@O6_:2@N2 132374 0.977 3.94 0.815 60 :1@N7_:2@O6 132225 0.976 4.01 0.794 61 :1@O6_:2@N3 132225 0.976 4.59 0.69 62 :1@N9_:2@N1 132133 0.975 4.95 0.626 63 :1@C4_:2@O6 132008 0.974 5.05 0.681 64 :1@N9_:2@N3 131573 0.971 5.02 0.666 65 :1@C6_:2@N9 131528 0.97 5.35 0.569 66 :1@N2_:2@C4 131498 0.97 5.21 0.816 67 :1@C2_:2@N2 131497 0.97 5.13 0.814 68 :1@C8_:2@N1 131375 0.969 4.51 0.75 69 :1@C2_:2@C5 131169 0.968 5.14 0.791 70 :1@C5_:2@N2 131088 0.967 4.59 0.736 71 :1@C8_:2@C8 130787 0.965 5.03 0.828 72 :1@C2_:2@C8 130678 0.964 5.47 0.699 73 :1@N7_:2@C2 130563 0.963 4.4 0.825 74 :1@C8_:2@N9 130527 0.963 5.25 0.739 75 :1@O6_:2@N1 130031 0.959 4.2 0.814 76 :1@C6_:2@C5 129926 0.959 4.77 0.738 77 :1@O6_:2@C4 129901 0.958 5.16 0.651 78 :1@N9_:2@C2 129876 0.958 5.15 0.686 79 :1@C5_:2@C8 129448 0.955 5.21 0.696 80 :1@N1_:2@N1 129405 0.955 4.77 0.86 81 :1@C4_:2@N2 129404 0.955 5.26 0.67 82 :1@C5_:2@O6 129365 0.954 4.53 0.73 83 :1@N7_:2@N3 129293 0.954 4.75 0.804 84 :1@C5_:2@N7 129111 0.953 4.82 0.763 85 :1@C6_:2@C6 128913 0.951 4.55 0.789 86 :1@N7_:2@N9 128609 0.949 5.39 0.718 87 :1@N7_:2@N7 128246 0.946 4.74 0.822 88 :1@N3_:2@N2 128104 0.945 5.55 0.69 89 :1@C2_:2@N1 128033 0.945 5.27 0.837 90 :1@N1_:2@C5 127782 0.943 5.12 0.782 91 :1@C8_:2@C2 127225 0.939 4.93 0.814 92 :1@C8_:2@N3 126499 0.933 5.09 0.766 93 :1@O6_:2@C6 125586 0.927 4.78 0.823 94 :1@N1_:2@C6 125221 0.924 5.17 0.867 95 :1@N7_:2@N2 124664 0.92 4.85 0.913 96 :1@C2_:2@C6 123932 0.914 5.44 0.816 97 :1@N7_:2@C8 123921 0.914 5.34 0.733 98 :1@C6_:2@O6 123812 0.913 5.04 0.88 99 :1@C2_:2@N7 123754 0.913 5.6 0.766 100 :1@O6_:2@C5 123640 0.912 5.23 0.704 101 :1@N2_:2@C2 121994 0.9 5.37 0.906 102 :1@C6_:2@N7 120732 0.891 5.51 0.735 103 :1@N1_:2@C8 120503 0.889 5.84 0.648 104 :1@O6_:2@O6 119335 0.88 5.15 0.946 105 :1@C6_:2@C8 118991 0.878 5.77 0.607 106 :1@N2_:2@C8 117926 0.87 5.93 0.698 107 :1@N3_:2@O6 117701 0.868 5.83 0.691 108 :1@O6_:2@N9 117260 0.865 5.98 0.519 109 :1@N1_:2@N7 115697 0.854 5.79 0.764 110 :1@N9_:2@N2 115393 0.851 5.8 0.753 111 :1@C8_:2@N2 113805 0.84 5.49 0.896 112 :1@N2_:2@N2 113646 0.838 5.49 0.908 113 :1@N2_:2@C5 111384 0.822 5.74 0.78 114 :1@N1_:2@O6 104099 0.768 5.66 0.853 115 :1@O6_:2@N7 100510 0.742 6 0.663 116 :1@N2_:2@N1 96002 0.708 5.75 0.818 117 :1@C2_:2@O6 93342 0.689 5.9 0.734 118 :1@N2_:2@N7 90409 0.667 6.05 0.705 119 :1@O6_:2@C8 86099 0.635 6.29 0.498 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0209 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 135545 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 135545 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 135545 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 135545 COM "COM" (double, distance), size is 135545 v_base1 "v_base1" (vector, vector), size is 135545 v_base2 "v_base2" (vector, vector), size is 135545 normalangle "normalangle" (double), size is 135545 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: 2.7770 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.