CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/04/15 16:15:19 | Available memory: 979.152 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.c2] Reading '../ctraj.c2' 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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111593 of 111593) Coordinate processing will occur on 111593 frames. TIME: Run Initialization took 0.0027 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.c2 (1-111593, 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 111593 frames and processed 111593 frames. TIME: Trajectory processing: 1.9493 s TIME: Avg. throughput= 57247.7593 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 112.841 118 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 111261 0.997 4.09 0.49 2 :1@C4_:2@C8 111058 0.995 3.94 0.595 3 :1@N3_:2@N9 110896 0.994 3.92 0.562 4 :1@N3_:2@C4 110848 0.993 4.24 0.518 5 :1@C4_:2@C4 110664 0.992 4.27 0.475 6 :1@N9_:2@C8 110585 0.991 4.21 0.517 7 :1@N3_:2@C8 110526 0.99 4.1 0.653 8 :1@N9_:2@N9 110515 0.99 4.66 0.418 9 :1@C4_:2@C5 110379 0.989 4.25 0.467 10 :1@N3_:2@C5 110342 0.989 4.59 0.521 11 :1@C2_:2@C4 110320 0.989 3.95 0.594 12 :1@C4_:2@N7 110301 0.988 4.06 0.537 13 :1@N1_:2@C4 110259 0.988 3.81 0.636 14 :1@N1_:2@N3 110244 0.988 3.86 0.709 15 :1@N3_:2@N7 110215 0.988 4.53 0.616 16 :1@C5_:2@N9 110184 0.987 4.33 0.481 17 :1@C6_:2@N3 110135 0.987 4.21 0.655 18 :1@N3_:2@N3 110120 0.987 4.72 0.543 19 :1@C2_:2@N3 110071 0.986 4.13 0.626 20 :1@C2_:2@N9 110059 0.986 3.92 0.639 21 :1@C6_:2@C4 110038 0.986 3.93 0.539 22 :1@C4_:2@N3 110035 0.986 4.93 0.581 23 :1@N1_:2@N9 110016 0.986 4.19 0.669 24 :1@N9_:2@N7 109982 0.986 4.32 0.501 25 :1@C5_:2@C8 109954 0.985 4.13 0.552 26 :1@C5_:2@C4 109952 0.985 4.13 0.474 27 :1@N9_:2@C4 109949 0.985 5.01 0.535 28 :1@C6_:2@N9 109874 0.985 4.43 0.579 29 :1@C5_:2@N7 109807 0.984 3.86 0.549 30 :1@C5_:2@C5 109734 0.983 3.84 0.438 31 :1@C5_:2@N3 109727 0.983 4.74 0.617 32 :1@N1_:2@C2 109721 0.983 4.1 0.717 33 :1@C8_:2@C8 109712 0.983 4.51 0.548 34 :1@C6_:2@C5 109705 0.983 3.77 0.528 35 :1@N9_:2@C5 109658 0.983 4.82 0.498 36 :1@N7_:2@C8 109599 0.982 4.53 0.528 37 :1@C6_:2@C2 109573 0.982 4.22 0.679 38 :1@C8_:2@N9 109507 0.981 5.13 0.517 39 :1@N1_:2@C5 109498 0.981 4.06 0.642 40 :1@N7_:2@N7 109481 0.981 4.04 0.553 41 :1@C8_:2@N7 109477 0.981 4.26 0.585 42 :1@N7_:2@N9 109460 0.981 5.02 0.521 43 :1@C2_:2@C5 109455 0.981 4.42 0.606 44 :1@O6_:2@C4 109450 0.981 4.37 0.595 45 :1@N7_:2@C5 109419 0.981 4.24 0.583 46 :1@C5_:2@C6 109383 0.98 4.22 0.528 47 :1@C6_:2@C6 109366 0.98 3.88 0.506 48 :1@C4_:2@C6 109333 0.98 4.96 0.518 49 :1@N1_:2@N1 109301 0.979 4.35 0.646 50 :1@C6_:2@N7 109291 0.979 4.19 0.69 51 :1@O6_:2@C5 109286 0.979 4.05 0.58 52 :1@C2_:2@C2 109277 0.979 4.71 0.634 53 :1@N7_:2@C4 109277 0.979 4.84 0.619 54 :1@O6_:2@N3 109262 0.979 4.48 0.754 55 :1@C6_:2@N1 109254 0.979 4.09 0.572 56 :1@C8_:2@C5 109248 0.979 4.75 0.632 57 :1@O6_:2@N1 109217 0.979 3.81 0.677 58 :1@C6_:2@C8 109203 0.979 4.52 0.656 59 :1@O6_:2@C6 109202 0.979 3.75 0.583 60 :1@O6_:2@C2 109071 0.977 4.14 0.8 61 :1@C5_:2@N1 109035 0.977 4.74 0.656 62 :1@C2_:2@C8 108969 0.976 4.36 0.715 63 :1@N1_:2@C6 108922 0.976 4.37 0.606 64 :1@N3_:2@C6 108906 0.976 5.42 0.505 65 :1@N2_:2@N3 108899 0.976 4.31 0.748 66 :1@C8_:2@C4 108792 0.975 5.25 0.653 67 :1@N2_:2@C4 108756 0.975 4.37 0.658 68 :1@C5_:2@C2 108744 0.974 4.94 0.687 69 :1@C5_:2@O6 108739 0.974 4.61 0.552 70 :1@C6_:2@O6 108723 0.974 4.35 0.579 71 :1@N7_:2@C6 108687 0.974 4.48 0.735 72 :1@N3_:2@C2 108641 0.974 5.41 0.571 73 :1@O6_:2@O6 108526 0.973 4 0.665 74 :1@C2_:2@N1 108496 0.972 5.13 0.592 75 :1@O6_:2@N9 108482 0.972 5.12 0.582 76 :1@N2_:2@N9 108400 0.971 4.27 0.682 77 :1@C2_:2@N7 108311 0.971 4.68 0.704 78 :1@C4_:2@C2 108304 0.971 5.43 0.653 79 :1@O6_:2@N7 108303 0.971 4.65 0.715 80 :1@C2_:2@C6 108302 0.971 5.06 0.574 81 :1@C4_:2@N1 108269 0.97 5.47 0.626 82 :1@C4_:2@O6 108174 0.969 5.52 0.517 83 :1@N1_:2@C8 108008 0.968 4.56 0.724 84 :1@N1_:2@N7 107740 0.965 4.54 0.744 85 :1@N9_:2@C6 107685 0.965 5.58 0.627 86 :1@C6_:2@N2 107528 0.964 4.91 0.799 87 :1@N3_:2@N1 107493 0.963 5.71 0.539 88 :1@N7_:2@O6 107378 0.962 4.55 0.684 89 :1@O6_:2@C8 107094 0.96 5.19 0.633 90 :1@N1_:2@O6 107047 0.959 5.07 0.628 91 :1@C8_:2@C6 106732 0.956 5.24 0.766 92 :1@N2_:2@C5 106685 0.956 5.09 0.65 93 :1@N1_:2@N2 106541 0.955 4.6 0.765 94 :1@N2_:2@C2 106219 0.952 4.96 0.712 95 :1@N7_:2@N1 105961 0.95 5.18 0.876 96 :1@C2_:2@N2 105779 0.948 5.29 0.694 97 :1@N2_:2@C8 105554 0.946 4.92 0.701 98 :1@C8_:2@O6 105286 0.943 5.39 0.723 99 :1@O6_:2@N2 105161 0.942 4.62 0.894 100 :1@N9_:2@N3 104549 0.937 5.79 0.704 101 :1@N7_:2@N3 104292 0.935 5.51 0.739 102 :1@N2_:2@N7 103496 0.927 5.39 0.706 103 :1@C2_:2@O6 103191 0.925 5.83 0.574 104 :1@N2_:2@C6 102678 0.92 5.73 0.655 105 :1@N2_:2@N1 102621 0.92 5.6 0.658 106 :1@N9_:2@O6 101828 0.912 5.94 0.568 107 :1@N3_:2@O6 101528 0.91 6.11 0.478 108 :1@N2_:2@N2 100597 0.901 5.29 0.71 109 :1@N7_:2@C2 100354 0.899 5.56 0.836 110 :1@C5_:2@N2 99102 0.888 5.7 0.698 111 :1@N3_:2@N2 95781 0.858 6.06 0.579 112 :1@C8_:2@N3 92816 0.832 5.92 0.767 113 :1@C8_:2@N1 88973 0.797 5.81 0.879 114 :1@N9_:2@N1 87016 0.78 6.05 0.727 115 :1@C4_:2@N2 86083 0.771 6.09 0.629 116 :1@N9_:2@C2 82089 0.736 6.07 0.778 117 :1@C8_:2@C2 74734 0.67 5.97 0.892 118 :1@N2_:2@O6 66583 0.597 6.29 0.66 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0161 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 111593 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 111593 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 111593 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 111593 COM "COM" (double, distance), size is 111593 v_base1 "v_base1" (vector, vector), size is 111593 v_base2 "v_base2" (vector, vector), size is 111593 normalangle "normalangle" (double), size is 111593 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: 2.2441 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.