CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:02:44 | Available memory: 54704.2 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,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, 97577 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 97577 of 97577) Coordinate processing will occur on 97577 frames. TIME: Run Initialization took 0.0005 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.c3 (1-97577, 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 97577 frames and processed 97577 frames. TIME: Trajectory processing: 0.5800 s TIME: Avg. throughput= 168239.3976 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 82.6691 86 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C8 97070 0.995 4.3 0.545 2 :1@C4_:2@N9 97068 0.995 4.3 0.552 3 :1@N9_:2@N9 97033 0.994 4.78 0.46 4 :1@C4_:2@C8 97003 0.994 4.09 0.703 5 :1@C4_:2@N7 96819 0.992 4.17 0.662 6 :1@C4_:2@C4 96819 0.992 4.46 0.482 7 :1@C5_:2@N9 96793 0.992 4.52 0.667 8 :1@N9_:2@N7 96706 0.991 4.4 0.557 9 :1@C4_:2@C5 96660 0.991 4.38 0.519 10 :1@C5_:2@C4 96554 0.99 4.34 0.553 11 :1@C5_:2@C5 96487 0.989 4.03 0.513 12 :1@C6_:2@C4 96487 0.989 4.16 0.67 13 :1@C5_:2@C8 96486 0.989 4.29 0.719 14 :1@C5_:2@N7 96470 0.989 4.01 0.695 15 :1@C8_:2@C8 96465 0.989 4.57 0.64 16 :1@N9_:2@C4 96383 0.988 5.13 0.548 17 :1@N9_:2@C5 96364 0.988 4.91 0.552 18 :1@N3_:2@N9 96291 0.987 4.19 0.722 19 :1@N7_:2@N7 96274 0.987 4.16 0.717 20 :1@C6_:2@C5 96243 0.986 3.97 0.667 21 :1@N3_:2@C4 96242 0.986 4.45 0.636 22 :1@C8_:2@N7 96158 0.985 4.33 0.695 23 :1@N7_:2@C8 96121 0.985 4.61 0.687 24 :1@C8_:2@N9 96070 0.985 5.18 0.661 25 :1@N7_:2@C5 96012 0.984 4.38 0.698 26 :1@N1_:2@C4 96005 0.984 4.1 0.803 27 :1@N3_:2@C8 95947 0.983 4.28 0.86 28 :1@C5_:2@C6 95873 0.983 4.37 0.598 29 :1@C6_:2@N3 95860 0.982 4.44 0.695 30 :1@C4_:2@N3 95804 0.982 5.11 0.597 31 :1@N6_:2@C5 95791 0.982 4.26 0.738 32 :1@C5_:2@N3 95770 0.981 4.93 0.681 33 :1@N7_:2@C4 95756 0.981 4.95 0.771 34 :1@C6_:2@N9 95738 0.981 4.61 0.796 35 :1@C6_:2@C6 95734 0.981 4.04 0.636 36 :1@N3_:2@C5 95726 0.981 4.67 0.688 37 :1@C6_:2@N7 95700 0.981 4.34 0.85 38 :1@N7_:2@N9 95652 0.98 5.09 0.739 39 :1@C8_:2@C5 95635 0.98 4.84 0.725 40 :1@N6_:2@C4 95571 0.979 4.58 0.792 41 :1@N1_:2@C5 95545 0.979 4.23 0.87 42 :1@N6_:2@C6 95541 0.979 3.94 0.69 43 :1@N3_:2@N7 95533 0.979 4.6 0.811 44 :1@C2_:2@C4 95521 0.979 4.2 0.78 45 :1@C4_:2@C6 95497 0.979 5.02 0.637 46 :1@C6_:2@C2 95471 0.978 4.45 0.649 47 :1@C8_:2@C4 95422 0.978 5.33 0.744 48 :1@C6_:2@N1 95372 0.977 4.3 0.625 49 :1@N6_:2@N1 95326 0.977 4.04 0.665 50 :1@C5_:2@C2 95139 0.975 5.11 0.734 51 :1@C5_:2@N1 95138 0.975 4.92 0.712 52 :1@N6_:2@C2 95072 0.974 4.36 0.807 53 :1@C2_:2@N9 94931 0.973 4.23 0.875 54 :1@C5_:2@N6 94850 0.972 4.69 0.719 55 :1@N7_:2@C6 94782 0.971 4.65 0.811 56 :1@N6_:2@N6 94757 0.971 4.1 0.885 57 :1@C6_:2@C8 94635 0.97 4.64 0.823 58 :1@C2_:2@C5 94632 0.97 4.5 0.845 59 :1@C6_:2@N6 94550 0.969 4.43 0.804 60 :1@N1_:2@N9 94293 0.966 4.47 0.874 61 :1@N1_:2@N1 94292 0.966 4.44 0.804 62 :1@N1_:2@C6 94279 0.966 4.38 0.845 63 :1@N6_:2@N7 94032 0.964 4.8 0.837 64 :1@C4_:2@N1 93173 0.955 5.56 0.748 65 :1@N9_:2@C6 93049 0.954 5.63 0.702 66 :1@N1_:2@N7 92987 0.953 4.67 0.949 67 :1@C2_:2@C8 92765 0.951 4.52 0.925 68 :1@C4_:2@N6 92314 0.946 5.49 0.67 69 :1@C2_:2@N7 92211 0.945 4.71 0.924 70 :1@N7_:2@N6 92172 0.945 4.65 0.777 71 :1@N7_:2@N1 92167 0.945 5.35 0.941 72 :1@C8_:2@C6 92032 0.943 5.34 0.838 73 :1@N3_:2@C6 91970 0.943 5.32 0.694 74 :1@C2_:2@C6 91583 0.939 4.92 0.811 75 :1@N1_:2@C8 91335 0.936 4.72 0.88 76 :1@N7_:2@N3 90048 0.923 5.6 0.908 77 :1@N1_:2@N6 89508 0.917 4.89 0.878 78 :1@N6_:2@C8 89428 0.916 5.26 0.719 79 :1@C8_:2@N6 89080 0.913 5.42 0.807 80 :1@N6_:2@N9 88853 0.911 5.16 0.705 81 :1@N7_:2@C2 85496 0.876 5.64 0.941 82 :1@N9_:2@N6 84895 0.87 5.91 0.666 83 :1@C2_:2@N6 82020 0.841 5.49 0.784 84 :1@N3_:2@N6 81121 0.831 5.86 0.645 85 :1@C8_:2@N3 74635 0.765 5.91 0.819 86 :1@C8_:2@N1 69507 0.712 5.83 0.895 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0051 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 97577 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 97577 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 97577 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 97577 COM "COM" (double, distance), size is 97577 v_base1 "v_base1" (vector), size is 97577 v_base2 "v_base2" (vector), size is 97577 normalangle "normalangle" (double), size is 97577 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: 0.7679 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.