CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:23:58 | Available memory: 7.081 GB INPUT: Reading input from '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-] Warning: Action specified before trajin/ensemble. Assuming trajin. 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*). Best-fit RMSD will be calculated, coords will be rotated and translated. [nativecontacts :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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] [vector v_base2 :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] [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 (1 total): 0: [traj] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 33050 of 33050) Coordinate processing will occur on 33050 frames. 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*](42) Reference mask: [:1,2&!@H*](42) 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :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. ----- ctraj.c1 (1-33050, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 110 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@N7' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@O6' Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@N2' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C4' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@O6' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@N2' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@O6' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N2' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@O6' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N2' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@O6' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@N2' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@O6' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@N2' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@O6' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@N2' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@O6' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@N2' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C4' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@O6' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@N2' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 33050 frames and processed 33050 frames. TIME: Avg. throughput= 50869.3190 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 103.925 110 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@C4 33024 0.999 4.25 0.402 2 :2@C4_:1@C4 33013 0.999 4.53 0.478 3 :2@N9_:1@N9 33012 0.999 4.97 0.502 4 :2@N7_:1@C4 33009 0.999 4.4 0.688 5 :2@C5_:1@N9 32998 0.998 4.61 0.53 6 :2@C5_:1@C5 32985 0.998 4.26 0.571 7 :2@C5_:1@N3 32984 0.998 4.48 0.509 8 :2@C4_:1@N3 32980 0.998 4.48 0.57 9 :2@C6_:1@C4 32970 0.998 4.44 0.675 10 :2@N7_:1@N9 32965 0.997 4.46 0.58 11 :2@C4_:1@N9 32958 0.997 4.91 0.529 12 :2@C6_:1@C6 32950 0.997 4.05 0.551 13 :2@C6_:1@C5 32948 0.997 4.14 0.512 14 :2@N9_:1@C4 32940 0.997 4.81 0.798 15 :2@N6_:1@C5 32928 0.996 4.2 0.665 16 :2@N6_:1@C6 32909 0.996 4.03 0.627 17 :2@C6_:1@N1 32905 0.996 4.26 0.624 18 :2@C5_:1@C6 32889 0.995 4.47 0.837 19 :2@C8_:1@N9 32885 0.995 4.64 0.699 20 :2@C4_:1@C5 32877 0.995 4.78 0.709 21 :2@C5_:1@C8 32876 0.995 4.79 0.631 22 :2@N6_:1@O6 32863 0.994 4.05 0.687 23 :2@C8_:1@C4 32860 0.994 4.67 0.94 24 :2@N7_:1@C5 32854 0.994 4.48 0.867 25 :2@C6_:1@N3 32850 0.994 4.69 0.772 26 :2@C5_:1@N7 32848 0.994 4.63 0.645 27 :2@N3_:1@N3 32838 0.994 4.73 0.639 28 :2@N3_:1@C4 32838 0.994 4.98 0.598 29 :2@N6_:1@C4 32835 0.993 4.77 0.851 30 :2@C5_:1@C2 32824 0.993 4.61 0.691 31 :2@N7_:1@N3 32824 0.993 4.78 0.751 32 :2@N1_:1@N1 32823 0.993 4.2 0.713 33 :2@N1_:1@C6 32812 0.993 4.21 0.671 34 :2@C6_:1@O6 32803 0.993 4.31 0.783 35 :2@N1_:1@C5 32803 0.993 4.56 0.776 36 :2@C6_:1@N7 32790 0.992 4.58 0.688 37 :2@N6_:1@N7 32789 0.992 4.46 0.761 38 :2@C6_:1@C2 32775 0.992 4.55 0.691 39 :2@C6_:1@N9 32766 0.991 5 0.846 40 :2@C5_:1@N1 32738 0.991 4.61 0.854 41 :2@N1_:1@C4 32718 0.99 4.83 0.943 42 :2@N1_:1@C2 32700 0.989 4.52 0.86 43 :2@C2_:1@N3 32659 0.988 4.85 0.874 44 :2@N9_:1@N3 32644 0.988 4.72 0.958 45 :2@C4_:1@C8 32633 0.987 5.34 0.648 46 :2@C2_:1@C4 32600 0.986 5.03 0.84 47 :2@N6_:1@N1 32596 0.986 4.45 0.808 48 :2@C2_:1@C2 32552 0.985 4.54 0.804 49 :2@N1_:1@N3 32531 0.984 4.86 0.998 50 :2@C4_:1@C2 32529 0.984 4.57 0.886 51 :2@C6_:1@C8 32528 0.984 5.02 0.806 52 :2@N9_:1@C8 32497 0.983 5.49 0.615 53 :2@C4_:1@N7 32488 0.983 5.32 0.684 54 :2@C2_:1@C5 32421 0.981 5.01 0.772 55 :2@N1_:1@O6 32381 0.98 4.37 0.823 56 :2@N6_:1@C8 32376 0.98 5.09 0.85 57 :2@N7_:1@C8 32347 0.979 4.51 0.694 58 :2@C2_:1@N1 32287 0.977 4.44 0.823 59 :2@N3_:1@C5 32285 0.977 5.19 0.709 60 :2@C8_:1@N3 32281 0.977 4.83 1.01 61 :2@C2_:1@C6 32178 0.974 4.7 0.799 62 :2@N3_:1@C2 32133 0.972 4.57 0.835 63 :2@N7_:1@N7 32097 0.971 4.55 0.793 64 :2@N7_:1@C6 32045 0.97 4.94 1 65 :2@N6_:1@N9 31971 0.967 5.29 0.872 66 :2@C5_:1@O6 31967 0.967 4.94 0.981 67 :2@C4_:1@C6 31928 0.966 4.9 0.992 68 :2@N9_:1@C5 31888 0.965 5.24 0.925 69 :2@C8_:1@C8 31844 0.964 4.93 0.702 70 :2@N6_:1@C2 31830 0.963 4.92 0.956 71 :2@N3_:1@N9 31731 0.96 5.48 0.783 72 :2@C8_:1@C5 31727 0.96 4.99 1.01 73 :2@N6_:1@N3 31718 0.96 5.13 0.976 74 :2@C4_:1@N1 31709 0.959 4.74 1.07 75 :2@C6_:1@N2 31686 0.959 5.14 0.781 76 :2@N1_:1@N7 31678 0.958 5.11 0.895 77 :2@C5_:1@N2 31666 0.958 5.2 0.755 78 :2@N7_:1@C2 31653 0.958 5.09 0.884 79 :2@N1_:1@N2 31560 0.955 4.9 0.934 80 :2@C2_:1@N2 31392 0.95 4.69 0.913 81 :2@C4_:1@N2 31105 0.941 4.9 0.937 82 :2@N3_:1@N1 31084 0.941 4.68 1.01 83 :2@N7_:1@N1 31033 0.939 5.16 0.972 84 :2@N3_:1@C6 30919 0.936 5.03 0.919 85 :2@C8_:1@N7 30859 0.934 5.16 0.805 86 :2@N9_:1@N7 30753 0.93 5.65 0.726 87 :2@N3_:1@N2 30485 0.922 4.63 0.903 88 :2@C2_:1@O6 30466 0.922 4.92 0.961 89 :2@N9_:1@C2 30373 0.919 4.92 1.19 90 :2@N3_:1@N7 29562 0.894 5.76 0.767 91 :2@C2_:1@N7 29231 0.884 5.55 0.898 92 :2@C8_:1@C2 29014 0.878 5.13 1.08 93 :2@N7_:1@O6 28762 0.87 5.35 0.973 94 :2@N1_:1@N9 28513 0.863 5.32 0.99 95 :2@C4_:1@O6 28040 0.848 5.31 1.03 96 :2@N1_:1@C8 28002 0.847 5.43 0.936 97 :2@N3_:1@C8 27830 0.842 5.79 0.806 98 :2@N6_:1@N2 27674 0.837 5.43 0.988 99 :2@C2_:1@N9 27393 0.829 5.45 0.945 100 :2@C8_:1@C6 27163 0.822 5.31 1.05 101 :2@N3_:1@O6 27087 0.82 5.34 1.03 102 :2@N7_:1@N2 26898 0.814 5.55 0.807 103 :2@N9_:1@N2 26662 0.807 5.03 1.14 104 :2@N9_:1@C6 26490 0.802 5.31 1.05 105 :2@N9_:1@N1 26403 0.799 5.1 1.18 106 :2@C8_:1@N1 25444 0.77 5.26 1.06 107 :2@C2_:1@C8 24487 0.741 5.63 0.94 108 :2@C8_:1@N2 23624 0.715 5.34 0.908 109 :2@C8_:1@O6 19359 0.586 5.53 0.774 110 :2@N9_:1@O6 18006 0.545 5.45 0.734 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 33050, 'v_base2' size 33050, output size 33050 TIME: Analyses took 0.0049 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 33050 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 33050 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 33050 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 33050 COM "COM" (double, distance), size is 33050 v_base1 "v_base1" (vector, vector), size is 33050 v_base2 "v_base2" (vector, vector), size is 33050 normalangle "normalangle" (double), size is 33050 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.6497 s ( 99.18%) TIME: Action Post : 0.0003 s ( 0.05%) TIME: Analysis : 0.0049 s ( 0.75%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6551 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.7911 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.