CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:16:00 | Available memory: 52205.3 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.c1] Reading '../ctraj.c1' 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, 115245 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 115245 of 115245) Coordinate processing will occur on 115245 frames. TIME: Run Initialization took 0.0004 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.c1 (1-115245, 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 75 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@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@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@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@C4' 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@N6' to ':2@N7' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' 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@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 115245 frames and processed 115245 frames. TIME: Trajectory processing: 0.6836 s TIME: Avg. throughput= 168579.2649 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 65.329 75 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N7 114203 0.991 4.66 0.738 2 :1@N9_:2@C5 113656 0.986 4.47 0.598 3 :1@N9_:2@C8 113613 0.986 5.11 0.721 4 :1@N9_:2@N9 113410 0.984 5.3 0.559 5 :1@C4_:2@C5 112591 0.977 4.6 0.675 6 :1@N9_:2@C4 112230 0.974 4.85 0.577 7 :1@C4_:2@N7 112148 0.973 4.82 0.764 8 :1@C8_:2@N7 111702 0.969 4.78 0.949 9 :1@C8_:2@C5 111505 0.968 4.6 0.715 10 :1@N9_:2@C6 111441 0.967 4.44 0.677 11 :1@N9_:2@N6 111044 0.964 4.65 0.72 12 :1@C4_:2@N6 110927 0.963 4.34 0.79 13 :1@C5_:2@C5 110823 0.962 4.84 0.711 14 :1@C4_:2@C6 110711 0.961 4.34 0.759 15 :1@C5_:2@N6 110417 0.958 4.07 0.801 16 :1@C4_:2@C4 110074 0.955 5.13 0.658 17 :1@N7_:2@C5 109885 0.953 4.86 0.724 18 :1@C5_:2@N7 109829 0.953 5.09 0.817 19 :1@C8_:2@N6 109804 0.953 4.49 0.863 20 :1@N7_:2@N6 109761 0.952 4.21 0.854 21 :1@C8_:2@C6 109695 0.952 4.44 0.759 22 :1@C5_:2@C6 109610 0.951 4.35 0.767 23 :1@C4_:2@C8 109007 0.946 5.42 0.738 24 :1@N7_:2@C6 108979 0.946 4.44 0.761 25 :1@N7_:2@N7 108494 0.941 5.07 0.927 26 :1@N3_:2@C5 108201 0.939 4.85 0.782 27 :1@C4_:2@N9 108043 0.938 5.68 0.607 28 :1@N3_:2@N7 107536 0.933 5.07 0.887 29 :1@N9_:2@N1 107419 0.932 4.72 0.835 30 :1@C6_:2@N6 107364 0.932 4.18 0.891 31 :1@N9_:2@N3 107219 0.93 5.14 0.725 32 :1@N3_:2@C6 106453 0.924 4.61 0.864 33 :1@N3_:2@N6 106431 0.924 4.63 0.912 34 :1@C4_:2@N1 105681 0.917 4.57 0.894 35 :1@C5_:2@C4 105594 0.916 5.52 0.679 36 :1@C6_:2@C6 105214 0.913 4.68 0.833 37 :1@N6_:2@N6 105103 0.912 4.51 0.925 38 :1@C8_:2@N1 105003 0.911 4.69 0.934 39 :1@N9_:2@C2 104831 0.91 4.98 0.856 40 :1@C5_:2@N1 104481 0.907 4.58 0.919 41 :1@N3_:2@C4 103641 0.899 5.28 0.734 42 :1@N7_:2@N1 103386 0.897 4.67 0.942 43 :1@C6_:2@C5 102966 0.893 5.33 0.727 44 :1@N1_:2@N6 102335 0.888 4.4 0.932 45 :1@C4_:2@N3 101916 0.884 5.34 0.738 46 :1@C2_:2@N6 101707 0.883 4.54 0.972 47 :1@C4_:2@C2 101013 0.877 4.99 0.878 48 :1@N3_:2@C8 100718 0.874 5.56 0.839 49 :1@C2_:2@C6 100362 0.871 4.75 0.886 50 :1@C6_:2@N7 100222 0.87 5.59 0.796 51 :1@C2_:2@C5 100020 0.868 5.22 0.797 52 :1@N6_:2@C6 99617 0.864 5.17 0.825 53 :1@N3_:2@N1 99394 0.862 4.7 0.966 54 :1@N1_:2@C6 99323 0.862 4.83 0.833 55 :1@C5_:2@C8 98760 0.857 5.78 0.723 56 :1@C6_:2@N1 98576 0.855 4.81 0.934 57 :1@N3_:2@N9 98095 0.851 5.78 0.683 58 :1@N1_:2@C5 96262 0.835 5.47 0.729 59 :1@C2_:2@N7 95419 0.828 5.41 0.917 60 :1@N3_:2@N3 94937 0.824 5.4 0.859 61 :1@C2_:2@N1 94304 0.818 4.8 1.04 62 :1@N3_:2@C2 94252 0.818 5.03 0.998 63 :1@N1_:2@N1 94203 0.817 4.92 0.989 64 :1@N1_:2@N7 90205 0.783 5.68 0.829 65 :1@C2_:2@C4 89009 0.772 5.7 0.717 66 :1@C2_:2@C2 83221 0.722 5.18 1.03 67 :1@N1_:2@C2 79345 0.688 5.46 0.917 68 :1@N6_:2@N7 76989 0.668 6.01 0.714 69 :1@N1_:2@C4 76058 0.66 6 0.582 70 :1@C2_:2@N3 75792 0.658 5.65 0.832 71 :1@C2_:2@C8 74240 0.644 5.86 0.808 72 :1@C6_:2@C8 68404 0.594 6.16 0.67 73 :1@C2_:2@N9 67281 0.584 6.13 0.634 74 :1@N1_:2@C8 55270 0.48 6.12 0.717 75 :1@N1_:2@N9 41461 0.36 6.38 0.513 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0058 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 115245 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 115245 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 115245 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 115245 COM "COM" (double, distance), size is 115245 v_base1 "v_base1" (vector), size is 115245 v_base2 "v_base2" (vector), size is 115245 normalangle "normalangle" (double), size is 115245 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: 0.8985 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.