CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 20:55:21 | Available memory: 52541.3 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.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,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, 183029 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 183029 of 183029) Coordinate processing will occur on 183029 frames. TIME: Run Initialization took 0.0007 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.c0 (1-183029, 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 86 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@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@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@N9' 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@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@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@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@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@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 183029 frames and processed 183029 frames. TIME: Trajectory processing: 1.1063 s TIME: Avg. throughput= 165446.6533 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 77.5973 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 181025 0.989 4.6 0.628 2 :1@N9_:2@C5 180598 0.987 4.99 0.575 3 :1@N9_:2@C4 179903 0.983 5.14 0.565 4 :1@N9_:2@N9 179778 0.982 5.12 0.677 5 :1@C4_:2@C4 179654 0.982 4.79 0.64 6 :1@C4_:2@C6 179292 0.98 4.85 0.681 7 :1@N9_:2@N7 179273 0.979 4.85 0.835 8 :1@C4_:2@N7 178885 0.977 4.64 0.897 9 :1@C5_:2@C6 178127 0.973 4.55 0.761 10 :1@N3_:2@C5 178027 0.973 4.68 0.699 11 :1@N9_:2@C8 177975 0.972 4.88 0.944 12 :1@C5_:2@C5 177044 0.967 4.52 0.916 13 :1@N3_:2@N7 176997 0.967 4.76 0.839 14 :1@N3_:2@C4 176785 0.966 4.8 0.749 15 :1@C4_:2@N9 176462 0.964 4.92 0.91 16 :1@C6_:2@C6 176441 0.964 4.36 0.836 17 :1@C5_:2@N1 176217 0.963 4.82 0.796 18 :1@N9_:2@C6 176072 0.962 5.4 0.709 19 :1@C4_:2@N3 175727 0.96 5.19 0.639 20 :1@C5_:2@N6 175575 0.959 4.76 0.806 21 :1@C4_:2@C8 175386 0.958 4.77 1.07 22 :1@C4_:2@N1 175373 0.958 5.19 0.888 23 :1@C4_:2@N6 175355 0.958 5.17 0.777 24 :1@C2_:2@C5 175182 0.957 4.7 0.821 25 :1@C6_:2@N1 175162 0.957 4.49 0.764 26 :1@N1_:2@C6 174971 0.956 4.5 0.794 27 :1@C6_:2@N6 174935 0.956 4.48 0.878 28 :1@C5_:2@C4 174621 0.954 4.82 0.886 29 :1@N1_:2@N1 174225 0.952 4.58 0.817 30 :1@N3_:2@C6 174120 0.951 4.91 0.882 31 :1@N1_:2@C5 174096 0.951 4.72 0.969 32 :1@N3_:2@N9 173632 0.949 4.89 1.03 33 :1@N3_:2@C8 173576 0.948 4.84 1.03 34 :1@C8_:2@C4 173382 0.947 5.33 0.873 35 :1@C5_:2@C2 173127 0.946 5.05 0.786 36 :1@C6_:2@C5 172647 0.943 4.56 1.02 37 :1@C2_:2@C6 172623 0.943 4.68 0.843 38 :1@C8_:2@C5 172574 0.943 5.07 0.888 39 :1@C2_:2@C4 172558 0.943 4.83 1.01 40 :1@C5_:2@N3 171122 0.935 5.11 0.748 41 :1@N1_:2@N6 170932 0.934 4.59 0.92 42 :1@C6_:2@C2 170703 0.933 4.77 0.803 43 :1@C2_:2@N7 170647 0.932 4.95 0.952 44 :1@N7_:2@C6 169687 0.927 4.86 0.945 45 :1@N6_:2@N1 169173 0.924 4.44 0.946 46 :1@C8_:2@C6 168914 0.923 5.35 0.843 47 :1@N1_:2@C4 168836 0.922 4.9 1.16 48 :1@N6_:2@N6 168427 0.92 4.42 1.05 49 :1@N6_:2@C6 168324 0.92 4.44 1.05 50 :1@N7_:2@N1 167813 0.917 5.19 0.977 51 :1@C6_:2@C4 166741 0.911 4.83 1.06 52 :1@N7_:2@C5 166101 0.908 4.74 1.03 53 :1@N7_:2@C4 165678 0.905 5.11 0.999 54 :1@C5_:2@N7 165657 0.905 4.57 1.08 55 :1@N9_:2@N6 165425 0.904 5.72 0.685 56 :1@C6_:2@N3 164521 0.899 4.97 0.937 57 :1@C8_:2@N9 164063 0.896 5.34 0.922 58 :1@C2_:2@N6 163867 0.895 4.81 1.09 59 :1@N3_:2@N6 163472 0.893 5.15 1.05 60 :1@N1_:2@N7 163284 0.892 5.08 1.04 61 :1@N6_:2@C2 161707 0.884 4.78 0.99 62 :1@N7_:2@N6 161615 0.883 4.93 0.91 63 :1@N7_:2@N3 161108 0.88 5.44 0.983 64 :1@C8_:2@N7 159468 0.871 4.78 1.04 65 :1@N7_:2@C2 159192 0.87 5.35 1.01 66 :1@C2_:2@C8 158879 0.868 5.09 1.1 67 :1@C5_:2@N9 158764 0.867 5.03 1.01 68 :1@C2_:2@N9 157835 0.862 5 1.22 69 :1@C6_:2@N7 157721 0.862 4.8 1.05 70 :1@C8_:2@N6 157574 0.861 5.53 0.802 71 :1@N6_:2@C5 153537 0.839 4.73 1.05 72 :1@C8_:2@C8 152726 0.834 4.89 0.988 73 :1@C5_:2@C8 151677 0.829 4.77 1.04 74 :1@C8_:2@N3 150854 0.824 5.58 0.929 75 :1@N7_:2@N7 150017 0.82 4.56 1.07 76 :1@C8_:2@N1 145378 0.794 5.54 0.921 77 :1@N7_:2@N9 144268 0.788 5.19 0.976 78 :1@N6_:2@C4 138249 0.755 4.94 0.996 79 :1@N7_:2@C8 137991 0.754 4.8 0.928 80 :1@C6_:2@C8 136569 0.746 5.01 0.981 81 :1@N6_:2@N7 135893 0.742 5.04 0.929 82 :1@N1_:2@C8 135756 0.742 5.16 1.05 83 :1@C6_:2@N9 134391 0.734 5 0.998 84 :1@N1_:2@N9 132842 0.726 5 1.17 85 :1@N6_:2@C8 115888 0.633 5.4 0.747 86 :1@N6_:2@N9 111877 0.611 5.29 0.73 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0128 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 183029 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 183029 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 183029 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 183029 COM "COM" (double, distance), size is 183029 v_base1 "v_base1" (vector), size is 183029 v_base2 "v_base2" (vector), size is 183029 normalangle "normalangle" (double), size is 183029 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: 1.5238 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.