CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:10 | Available memory: 1.735 GB INPUT: Reading input from 'pt-criteria.in' [parm ../noWAt.topo.hmr [traj]] Reading '../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 :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_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 :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 (1 total): 0: [traj] noWAt.topo.hmr, 65 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 166306 of 166306) Coordinate processing will occur on 166306 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*](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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c1 (1-166306, 1) ----- 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 90 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@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@C2' 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@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@C4' 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@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@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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 166306 frames and processed 166306 frames. TIME: Avg. throughput= 86104.7572 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 79.5461 90 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 164202 0.987 4.63 0.65 2 :1@C4_:2@C5 163935 0.986 4.64 0.636 3 :1@N9_:2@N7 163498 0.983 4.94 0.819 4 :1@C4_:2@C6 162977 0.98 4.33 0.653 5 :1@N9_:2@C4 162919 0.98 4.93 0.592 6 :1@C4_:2@N6 162914 0.98 4.37 0.719 7 :1@N9_:2@C6 162807 0.979 4.57 0.693 8 :1@C4_:2@N7 162150 0.975 5 0.802 9 :1@N3_:2@C5 162026 0.974 4.75 0.71 10 :1@C4_:2@C4 161965 0.974 5.12 0.616 11 :1@N9_:2@N9 161701 0.972 5.42 0.602 12 :1@N9_:2@N6 161583 0.972 4.82 0.77 13 :1@N3_:2@C6 161458 0.971 4.47 0.779 14 :1@N9_:2@C8 161385 0.97 5.35 0.776 15 :1@C5_:2@C6 161280 0.97 4.45 0.799 16 :1@N3_:2@N6 161117 0.969 4.48 0.847 17 :1@C5_:2@N6 160979 0.968 4.24 0.882 18 :1@C4_:2@N1 160238 0.964 4.53 0.806 19 :1@C5_:2@C5 159943 0.962 4.98 0.77 20 :1@N9_:2@N1 159643 0.96 4.77 0.791 21 :1@C6_:2@N6 159547 0.959 4.28 0.902 22 :1@N3_:2@C4 158526 0.953 5.23 0.683 23 :1@N9_:2@N3 158461 0.953 5.14 0.685 24 :1@C6_:2@C6 158432 0.953 4.73 0.823 25 :1@N3_:2@N7 157912 0.95 5.03 0.846 26 :1@C5_:2@N1 157834 0.949 4.58 0.883 27 :1@C8_:2@C5 157250 0.946 4.9 0.876 28 :1@C2_:2@N6 157202 0.945 4.38 0.939 29 :1@N9_:2@C2 157097 0.945 4.99 0.804 30 :1@N1_:2@N6 157051 0.944 4.37 0.879 31 :1@C8_:2@C6 157012 0.944 4.71 0.921 32 :1@C4_:2@C2 156166 0.939 4.94 0.838 33 :1@C2_:2@C6 156135 0.939 4.62 0.835 34 :1@C4_:2@N9 155793 0.937 5.73 0.606 35 :1@C4_:2@N3 155773 0.937 5.3 0.71 36 :1@N3_:2@N1 155245 0.933 4.61 0.909 37 :1@C4_:2@C8 154884 0.931 5.57 0.755 38 :1@N1_:2@C6 154570 0.929 4.81 0.782 39 :1@C8_:2@C4 154516 0.929 5.25 0.739 40 :1@C2_:2@C5 154386 0.928 5.14 0.752 41 :1@N7_:2@C6 154287 0.928 4.66 0.914 42 :1@C5_:2@C4 153479 0.923 5.55 0.676 43 :1@C6_:2@N1 153274 0.922 4.79 0.902 44 :1@C8_:2@N1 152846 0.919 4.84 0.963 45 :1@N6_:2@N6 152809 0.919 4.64 0.977 46 :1@N7_:2@N6 151966 0.914 4.47 1.03 47 :1@C8_:2@N6 151804 0.913 4.76 0.993 48 :1@C6_:2@C5 151373 0.91 5.41 0.745 49 :1@N7_:2@N1 151027 0.908 4.76 0.962 50 :1@C2_:2@N1 150221 0.903 4.7 0.997 51 :1@C5_:2@C2 149942 0.902 5.13 0.858 52 :1@N7_:2@C5 149877 0.901 5.07 0.834 53 :1@N1_:2@N1 149672 0.9 4.86 0.932 54 :1@C5_:2@N7 149532 0.899 5.29 0.857 55 :1@N3_:2@N9 149479 0.899 5.78 0.64 56 :1@N3_:2@N3 149238 0.897 5.36 0.82 57 :1@N3_:2@C2 149186 0.897 4.99 0.961 58 :1@N3_:2@C8 148957 0.896 5.58 0.792 59 :1@C8_:2@N3 148341 0.892 5.37 0.813 60 :1@C8_:2@C2 148280 0.892 5.09 0.95 61 :1@N1_:2@C5 147971 0.89 5.49 0.705 62 :1@C8_:2@N7 147460 0.887 5.1 1.01 63 :1@N6_:2@C6 147069 0.884 5.24 0.846 64 :1@N7_:2@C4 144821 0.871 5.59 0.72 65 :1@C8_:2@N9 144717 0.87 5.74 0.71 66 :1@C2_:2@N7 144577 0.869 5.39 0.881 67 :1@C5_:2@N3 143588 0.863 5.63 0.712 68 :1@N7_:2@C2 142825 0.859 5.19 0.94 69 :1@N6_:2@N1 141435 0.85 5.22 0.88 70 :1@C2_:2@C4 141344 0.85 5.68 0.665 71 :1@C6_:2@C2 137888 0.829 5.42 0.838 72 :1@C8_:2@C8 136592 0.821 5.53 0.869 73 :1@N7_:2@N7 136527 0.821 5.29 0.945 74 :1@N7_:2@N3 136163 0.819 5.65 0.794 75 :1@C2_:2@C2 135867 0.817 5.16 0.992 76 :1@C6_:2@N7 133332 0.802 5.68 0.79 77 :1@N1_:2@N7 130773 0.786 5.74 0.816 78 :1@C6_:2@C4 127495 0.767 5.98 0.605 79 :1@C5_:2@C8 125055 0.752 5.88 0.726 80 :1@C2_:2@N3 125054 0.752 5.66 0.787 81 :1@C5_:2@N9 124269 0.747 6.12 0.602 82 :1@N1_:2@C4 121553 0.731 6.03 0.565 83 :1@N6_:2@C5 121310 0.729 5.9 0.684 84 :1@C2_:2@C8 114606 0.689 5.93 0.763 85 :1@N7_:2@N9 113834 0.684 6.09 0.662 86 :1@N7_:2@C8 112119 0.674 5.8 0.776 87 :1@C2_:2@N9 108522 0.653 6.19 0.591 88 :1@N6_:2@N7 94295 0.567 6.06 0.701 89 :1@C6_:2@C8 84440 0.508 6.2 0.667 90 :1@N1_:2@C8 75393 0.453 6.17 0.698 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 166306, 'v_base2' size 166306, output size 166306 TIME: Analyses took 0.0143 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 166306 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 166306 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 166306 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 166306 COM "COM" (double, distance), size is 166306 v_base1 "v_base1" (vector, vector), size is 166306 v_base2 "v_base2" (vector, vector), size is 166306 normalangle "normalangle" (double), size is 166306 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.10%) TIME: Trajectory Process : 1.9314 s ( 99.15%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0143 s ( 0.74%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.9481 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: 2.4094 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.