CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:24:02 | Available memory: 7.033 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 28036 of 28036) Coordinate processing will occur on 28036 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 (1-28036, 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 28036 frames and processed 28036 frames. TIME: Avg. throughput= 50614.9949 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 105.353 110 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@C4 28024 1 4.23 0.38 2 :2@N9_:1@N9 28024 1 4.93 0.455 3 :2@C4_:1@C4 28022 1 4.46 0.422 4 :2@C5_:1@C5 28018 0.999 4.15 0.494 5 :2@C5_:1@N9 28015 0.999 4.65 0.499 6 :2@N9_:1@C4 28007 0.999 4.66 0.731 7 :2@N7_:1@N9 28004 0.999 4.41 0.497 8 :2@C6_:1@C5 28003 0.999 4.13 0.501 9 :2@C4_:1@C5 28000 0.999 4.67 0.64 10 :2@C6_:1@C4 27996 0.999 4.53 0.675 11 :2@C4_:1@N9 27996 0.999 4.96 0.509 12 :2@C8_:1@N9 27992 0.998 4.55 0.634 13 :2@N7_:1@C4 27986 0.998 4.32 0.655 14 :2@C4_:1@N3 27982 0.998 4.36 0.479 15 :2@N6_:1@C5 27979 0.998 4.23 0.672 16 :2@C6_:1@C6 27975 0.998 3.95 0.472 17 :2@C5_:1@N7 27975 0.998 4.55 0.58 18 :2@C5_:1@C8 27964 0.997 4.79 0.592 19 :2@N1_:1@C6 27954 0.997 4.13 0.583 20 :2@C5_:1@N3 27954 0.997 4.48 0.503 21 :2@N7_:1@C5 27946 0.997 4.33 0.787 22 :2@C5_:1@C6 27943 0.997 4.29 0.745 23 :2@N3_:1@C4 27931 0.996 4.95 0.575 24 :2@C6_:1@O6 27929 0.996 4.14 0.661 25 :2@N6_:1@N7 27922 0.996 4.42 0.743 26 :2@N1_:1@C5 27921 0.996 4.59 0.756 27 :2@C6_:1@N7 27917 0.996 4.56 0.684 28 :2@C8_:1@C4 27915 0.996 4.52 0.895 29 :2@N3_:1@N3 27909 0.995 4.59 0.546 30 :2@N6_:1@C6 27904 0.995 4.02 0.636 31 :2@N9_:1@N3 27903 0.995 4.52 0.878 32 :2@N1_:1@O6 27901 0.995 4.24 0.72 33 :2@N6_:1@O6 27885 0.995 3.94 0.627 34 :2@C4_:1@C6 27881 0.994 4.74 0.929 35 :2@C6_:1@N1 27864 0.994 4.2 0.593 36 :2@C4_:1@C2 27863 0.994 4.37 0.756 37 :2@N7_:1@C8 27862 0.994 4.44 0.585 38 :2@N7_:1@N7 27860 0.994 4.45 0.7 39 :2@N1_:1@N1 27853 0.993 4.09 0.639 40 :2@N6_:1@C4 27853 0.993 4.92 0.815 41 :2@C2_:1@C6 27849 0.993 4.59 0.715 42 :2@N3_:1@C2 27845 0.993 4.35 0.629 43 :2@C5_:1@N1 27840 0.993 4.46 0.8 44 :2@C2_:1@N1 27836 0.993 4.24 0.648 45 :2@N9_:1@C8 27832 0.993 5.49 0.558 46 :2@C6_:1@N3 27831 0.993 4.81 0.759 47 :2@C6_:1@N9 27830 0.993 5.14 0.823 48 :2@C5_:1@C2 27828 0.993 4.54 0.667 49 :2@N7_:1@N3 27801 0.992 4.76 0.75 50 :2@C4_:1@N1 27788 0.991 4.54 0.981 51 :2@N1_:1@C4 27787 0.991 4.94 0.947 52 :2@N3_:1@N1 27784 0.991 4.5 0.897 53 :2@N9_:1@C5 27777 0.991 5.11 0.889 54 :2@N3_:1@C5 27773 0.991 5.14 0.668 55 :2@C4_:1@N7 27771 0.991 5.29 0.653 56 :2@C2_:1@C2 27768 0.99 4.38 0.708 57 :2@C5_:1@O6 27750 0.99 4.77 0.915 58 :2@C4_:1@C8 27750 0.99 5.39 0.604 59 :2@C6_:1@C2 27728 0.989 4.59 0.694 60 :2@C2_:1@N3 27726 0.989 4.83 0.899 61 :2@C2_:1@C5 27715 0.989 5.02 0.727 62 :2@N1_:1@C2 27707 0.988 4.5 0.884 63 :2@C8_:1@C8 27695 0.988 4.88 0.643 64 :2@C2_:1@C4 27693 0.988 5.08 0.844 65 :2@C6_:1@C8 27648 0.986 5.08 0.807 66 :2@N3_:1@C6 27645 0.986 4.93 0.888 67 :2@C8_:1@C5 27596 0.984 4.85 0.968 68 :2@N1_:1@N3 27553 0.983 4.95 1.03 69 :2@N6_:1@N1 27549 0.983 4.54 0.806 70 :2@C8_:1@N3 27539 0.982 4.7 0.998 71 :2@N6_:1@C8 27529 0.982 5.12 0.849 72 :2@N7_:1@C6 27506 0.981 4.79 0.964 73 :2@N3_:1@N2 27492 0.981 4.45 0.745 74 :2@C4_:1@N2 27456 0.979 4.75 0.856 75 :2@C8_:1@N7 27394 0.977 5.09 0.786 76 :2@C2_:1@O6 27313 0.974 4.86 0.945 77 :2@C2_:1@N2 27283 0.973 4.52 0.814 78 :2@N9_:1@N7 27132 0.968 5.62 0.711 79 :2@C5_:1@N2 27059 0.965 5.16 0.746 80 :2@N9_:1@C2 27057 0.965 4.75 1.14 81 :2@N6_:1@N9 27049 0.965 5.43 0.839 82 :2@N1_:1@N7 26988 0.963 5.19 0.86 83 :2@N7_:1@C2 26928 0.96 5.04 0.9 84 :2@N3_:1@N9 26840 0.957 5.59 0.746 85 :2@N6_:1@C2 26772 0.955 5.13 0.867 86 :2@N1_:1@N2 26707 0.953 4.86 0.95 87 :2@C6_:1@N2 26705 0.953 5.19 0.77 88 :2@N6_:1@N3 26666 0.951 5.37 0.862 89 :2@N7_:1@N1 26567 0.948 5.04 0.979 90 :2@N7_:1@O6 25922 0.925 5.25 0.955 91 :2@C4_:1@O6 25867 0.923 5.23 1.02 92 :2@N3_:1@N7 25384 0.905 5.84 0.696 93 :2@C8_:1@C2 25269 0.901 4.99 1.08 94 :2@N3_:1@O6 25017 0.892 5.28 1.03 95 :2@C2_:1@N7 24902 0.888 5.67 0.798 96 :2@N9_:1@N2 24818 0.885 4.94 1.11 97 :2@C8_:1@C6 24755 0.883 5.21 1.03 98 :2@N9_:1@C6 24710 0.881 5.23 1.04 99 :2@N9_:1@N1 24658 0.88 5 1.15 100 :2@N1_:1@N9 23625 0.843 5.5 0.956 101 :2@N1_:1@C8 23256 0.83 5.58 0.886 102 :2@N3_:1@C8 23194 0.827 5.94 0.688 103 :2@N7_:1@N2 22906 0.817 5.56 0.811 104 :2@C8_:1@N1 22885 0.816 5.12 1.03 105 :2@N6_:1@N2 22654 0.808 5.68 0.834 106 :2@C2_:1@N9 22542 0.804 5.61 0.898 107 :2@C8_:1@N2 20792 0.742 5.23 0.884 108 :2@C2_:1@C8 19902 0.71 5.82 0.81 109 :2@C8_:1@O6 18628 0.664 5.49 0.76 110 :2@N9_:1@O6 17471 0.623 5.42 0.717 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 28036, 'v_base2' size 28036, output size 28036 TIME: Analyses took 0.0041 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 28036 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 28036 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 28036 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 28036 COM "COM" (double, distance), size is 28036 v_base1 "v_base1" (vector, vector), size is 28036 v_base2 "v_base2" (vector, vector), size is 28036 normalangle "normalangle" (double), size is 28036 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.5539 s ( 99.17%) TIME: Action Post : 0.0003 s ( 0.06%) TIME: Analysis : 0.0041 s ( 0.74%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5585 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: 0.6737 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.