CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 18:33:36 | Available memory: 50898.3 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,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_00001 Saving minimum observed distances in set 'Contacts_00001[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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :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] [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: [traj] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 15304 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 15304 of 15304) Coordinate processing will occur on 15304 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](41) Reference mask: [:1,2&!@H*](41) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c2 (1-15304, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 99 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@N6' 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@N6' 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@N6' 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@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' 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@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@C8' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N6' 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@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' 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@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' 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@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' 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@N6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 15304 frames and processed 15304 frames. TIME: Trajectory processing: 0.0982 s TIME: Avg. throughput= 155878.5484 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 89.9243 99 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 15298 1 4.36 0.531 2 :1@C4_:2@C6 15293 0.999 3.97 0.459 3 :1@N3_:2@C6 15291 0.999 4.11 0.555 4 :1@C4_:2@C4 15287 0.999 4.82 0.538 5 :1@N9_:2@C4 15286 0.999 4.62 0.519 6 :1@C4_:2@N6 15285 0.999 4.08 0.592 7 :1@N3_:2@C5 15282 0.999 4.35 0.515 8 :1@N3_:2@N6 15280 0.998 4.02 0.651 9 :1@N9_:2@C5 15270 0.998 4.5 0.611 10 :1@N9_:2@C6 15264 0.997 4.31 0.553 11 :1@C2_:2@N6 15257 0.997 3.89 0.68 12 :1@C4_:2@N1 15255 0.997 4.08 0.593 13 :1@C2_:2@C6 15248 0.996 4.33 0.652 14 :1@C5_:2@C6 15240 0.996 4.13 0.576 15 :1@N1_:2@N6 15236 0.996 3.93 0.639 16 :1@N3_:2@N7 15234 0.995 4.61 0.661 17 :1@C5_:2@N1 15228 0.995 3.99 0.605 18 :1@N9_:2@N3 15221 0.995 4.6 0.533 19 :1@N3_:2@C4 15221 0.995 5 0.616 20 :1@C4_:2@N3 15215 0.994 4.96 0.615 21 :1@C6_:2@C6 15206 0.994 4.4 0.631 22 :1@C6_:2@N1 15204 0.993 4.41 0.71 23 :1@N9_:2@N1 15202 0.993 4.25 0.586 24 :1@N1_:2@C6 15199 0.993 4.51 0.641 25 :1@C4_:2@C2 15198 0.993 4.54 0.674 26 :1@C6_:2@N6 15197 0.993 3.99 0.658 27 :1@N9_:2@N9 15191 0.993 5.31 0.659 28 :1@N3_:2@N1 15185 0.992 4.55 0.726 29 :1@C2_:2@C5 15184 0.992 4.79 0.661 30 :1@C5_:2@N6 15183 0.992 4.08 0.648 31 :1@N9_:2@C2 15179 0.992 4.35 0.623 32 :1@C5_:2@C2 15170 0.991 4.56 0.713 33 :1@N9_:2@N6 15148 0.99 4.73 0.662 34 :1@C5_:2@C5 15136 0.989 4.83 0.692 35 :1@C4_:2@N7 15129 0.989 4.91 0.736 36 :1@C8_:2@N3 15079 0.985 4.68 0.672 37 :1@C8_:2@N1 15077 0.985 4.2 0.628 38 :1@N7_:2@N1 15076 0.985 4.08 0.618 39 :1@C5_:2@N3 15075 0.985 5.24 0.705 40 :1@C5_:2@C4 15075 0.985 5.3 0.692 41 :1@C8_:2@C2 15074 0.985 4.23 0.637 42 :1@N7_:2@C2 15067 0.985 4.38 0.705 43 :1@N1_:2@N1 15049 0.983 4.8 0.776 44 :1@C4_:2@N9 15044 0.983 5.58 0.622 45 :1@C2_:2@N1 15034 0.982 4.8 0.807 46 :1@N6_:2@N1 15023 0.982 4.92 0.764 47 :1@C8_:2@C4 15020 0.981 4.99 0.753 48 :1@C8_:2@C6 15018 0.981 4.58 0.655 49 :1@N9_:2@N7 15018 0.981 5.1 0.842 50 :1@C2_:2@N7 15014 0.981 4.99 0.79 51 :1@N3_:2@C8 14991 0.98 5.3 0.707 52 :1@N7_:2@C6 14974 0.978 4.52 0.673 53 :1@N6_:2@N6 14970 0.978 4.53 0.79 54 :1@C8_:2@C5 14961 0.978 4.99 0.77 55 :1@N3_:2@C2 14948 0.977 5.11 0.759 56 :1@N7_:2@N3 14928 0.975 5.08 0.776 57 :1@N1_:2@C5 14917 0.975 5.23 0.712 58 :1@C6_:2@C5 14915 0.975 5.24 0.734 59 :1@N6_:2@C6 14906 0.974 5.06 0.727 60 :1@N3_:2@N9 14887 0.973 5.58 0.664 61 :1@N3_:2@N3 14852 0.97 5.4 0.705 62 :1@N7_:2@N6 14843 0.97 4.71 0.768 63 :1@C6_:2@C2 14831 0.969 5.2 0.77 64 :1@C4_:2@C8 14814 0.968 5.54 0.729 65 :1@C8_:2@N6 14811 0.968 5.01 0.734 66 :1@N9_:2@C8 14784 0.966 5.47 0.832 67 :1@N7_:2@C5 14751 0.964 5.2 0.784 68 :1@N7_:2@C4 14679 0.959 5.4 0.791 69 :1@C2_:2@C4 14463 0.945 5.58 0.698 70 :1@C5_:2@N7 14432 0.943 5.51 0.822 71 :1@C2_:2@C2 14054 0.918 5.52 0.761 72 :1@N1_:2@N7 13965 0.913 5.53 0.852 73 :1@C8_:2@N9 13900 0.908 5.76 0.876 74 :1@N1_:2@C2 13820 0.903 5.6 0.723 75 :1@C6_:2@C4 13562 0.886 5.84 0.661 76 :1@N6_:2@C2 13531 0.884 5.64 0.766 77 :1@C2_:2@C8 13465 0.88 5.74 0.821 78 :1@C8_:2@N7 13353 0.873 5.68 0.877 79 :1@C6_:2@N7 13317 0.87 5.73 0.841 80 :1@C6_:2@N3 13203 0.863 5.85 0.647 81 :1@N1_:2@C4 12995 0.849 5.94 0.638 82 :1@C2_:2@N3 12825 0.838 5.88 0.661 83 :1@N6_:2@C5 12652 0.827 5.87 0.729 84 :1@C5_:2@N9 12312 0.804 6.05 0.684 85 :1@C2_:2@N9 11984 0.783 6.04 0.744 86 :1@N7_:2@N7 11952 0.781 5.86 0.823 87 :1@N1_:2@N3 11331 0.74 6.08 0.565 88 :1@C8_:2@C8 11308 0.739 5.9 0.906 89 :1@C5_:2@C8 11238 0.734 6 0.742 90 :1@N7_:2@N9 10249 0.67 6.03 0.815 91 :1@N1_:2@C8 9163 0.599 6.08 0.844 92 :1@N6_:2@N3 8900 0.582 6.18 0.591 93 :1@N6_:2@C4 8368 0.547 6.23 0.585 94 :1@C6_:2@C8 7578 0.495 6.12 0.748 95 :1@N6_:2@N7 7563 0.494 6.03 0.838 96 :1@N7_:2@C8 7530 0.492 6 0.779 97 :1@C6_:2@N9 7058 0.461 6.25 0.623 98 :1@N1_:2@N9 6922 0.452 6.25 0.716 99 :1@N6_:2@C8 2801 0.183 6.17 0.767 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0008 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 15304 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 15304 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 15304 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 15304 COM "COM" (double, distance), size is 15304 v_base1 "v_base1" (vector), size is 15304 v_base2 "v_base2" (vector), size is 15304 normalangle "normalangle" (double), size is 15304 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' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.1593 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.