CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:18:20 | Available memory: 1.727 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.c2] Reading '../ctraj.c2' 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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 113220 of 113220) Coordinate processing will occur on 113220 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.c2 (1-113220, 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 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 113220 frames and processed 113220 frames. TIME: Avg. throughput= 83999.6973 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 83.2165 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 113050 0.998 4.23 0.491 2 :1@N3_:2@N9 112866 0.997 4.06 0.57 3 :1@C4_:2@C8 112834 0.997 4.03 0.621 4 :1@N3_:2@C4 112677 0.995 4.34 0.541 5 :1@N3_:2@C8 112612 0.995 4.2 0.713 6 :1@N9_:2@C8 112504 0.994 4.25 0.532 7 :1@C2_:2@N9 112433 0.993 4.12 0.716 8 :1@C2_:2@C4 112358 0.992 4.09 0.66 9 :1@N9_:2@N9 112327 0.992 4.75 0.45 10 :1@C4_:2@C4 112189 0.991 4.38 0.448 11 :1@N3_:2@N7 112139 0.99 4.57 0.698 12 :1@N3_:2@C5 112060 0.99 4.62 0.598 13 :1@C4_:2@N7 111978 0.989 4.1 0.58 14 :1@C5_:2@N9 111956 0.989 4.49 0.56 15 :1@N1_:2@N9 111939 0.989 4.41 0.731 16 :1@N1_:2@C4 111903 0.988 4.01 0.651 17 :1@C4_:2@C5 111791 0.987 4.3 0.458 18 :1@C6_:2@C4 111716 0.987 4.1 0.544 19 :1@C5_:2@C4 111713 0.987 4.3 0.505 20 :1@N9_:2@N7 111644 0.986 4.32 0.516 21 :1@N9_:2@C4 111624 0.986 5.1 0.544 22 :1@C5_:2@C8 111519 0.985 4.25 0.619 23 :1@C6_:2@N9 111518 0.985 4.57 0.65 24 :1@C4_:2@N3 111518 0.985 5.06 0.588 25 :1@C2_:2@C5 111476 0.985 4.48 0.743 26 :1@N9_:2@C5 111452 0.984 4.86 0.521 27 :1@C5_:2@C5 111447 0.984 3.96 0.445 28 :1@C6_:2@N3 111375 0.984 4.38 0.628 29 :1@C5_:2@N7 111345 0.983 3.95 0.599 30 :1@C5_:2@N3 111318 0.983 4.91 0.669 31 :1@C6_:2@C5 111254 0.983 3.9 0.552 32 :1@C2_:2@C8 111171 0.982 4.5 0.807 33 :1@N1_:2@C5 111103 0.981 4.18 0.738 34 :1@C8_:2@C8 111070 0.981 4.57 0.575 35 :1@C8_:2@N9 111045 0.981 5.24 0.585 36 :1@N7_:2@C5 111042 0.981 4.36 0.623 37 :1@N7_:2@N7 110963 0.98 4.12 0.607 38 :1@N7_:2@C4 110956 0.98 4.99 0.701 39 :1@N6_:2@C4 110944 0.98 4.56 0.654 40 :1@C5_:2@C6 110933 0.98 4.31 0.523 41 :1@C8_:2@N7 110908 0.98 4.29 0.607 42 :1@C4_:2@C6 110882 0.979 4.98 0.563 43 :1@C6_:2@C2 110848 0.979 4.39 0.621 44 :1@C8_:2@C5 110845 0.979 4.82 0.67 45 :1@N7_:2@N9 110834 0.979 5.16 0.625 46 :1@N7_:2@C8 110830 0.979 4.62 0.6 47 :1@C6_:2@C6 110825 0.979 3.98 0.538 48 :1@N6_:2@C5 110789 0.979 4.21 0.62 49 :1@C6_:2@N7 110759 0.978 4.29 0.74 50 :1@C6_:2@N1 110648 0.977 4.25 0.562 51 :1@C8_:2@C4 110610 0.977 5.36 0.702 52 :1@N7_:2@C6 110587 0.977 4.63 0.754 53 :1@N6_:2@C6 110583 0.977 3.87 0.578 54 :1@C5_:2@C2 110561 0.977 5.09 0.729 55 :1@C5_:2@N1 110475 0.976 4.88 0.67 56 :1@N6_:2@N1 110470 0.976 3.97 0.591 57 :1@N6_:2@C2 110388 0.975 4.32 0.746 58 :1@N1_:2@C6 110376 0.975 4.37 0.763 59 :1@C2_:2@N7 110371 0.975 4.75 0.825 60 :1@C6_:2@C8 110358 0.975 4.62 0.706 61 :1@C5_:2@N6 110329 0.974 4.64 0.602 62 :1@N1_:2@N1 110233 0.974 4.42 0.723 63 :1@N6_:2@N6 110071 0.972 4.05 0.765 64 :1@C6_:2@N6 110052 0.972 4.4 0.7 65 :1@N1_:2@N7 109569 0.968 4.68 0.84 66 :1@N7_:2@N6 109543 0.968 4.65 0.734 67 :1@N1_:2@C8 109512 0.967 4.74 0.782 68 :1@N9_:2@C6 109472 0.967 5.61 0.658 69 :1@N6_:2@N7 109240 0.965 4.78 0.748 70 :1@N3_:2@C6 109134 0.964 5.34 0.615 71 :1@C4_:2@N1 109100 0.964 5.55 0.672 72 :1@C8_:2@C6 109063 0.963 5.35 0.808 73 :1@C2_:2@C6 109021 0.963 4.98 0.741 74 :1@C4_:2@N6 108565 0.959 5.49 0.586 75 :1@N7_:2@N1 108067 0.954 5.37 0.909 76 :1@N6_:2@N9 107368 0.948 5.24 0.635 77 :1@C8_:2@N6 106792 0.943 5.44 0.779 78 :1@N6_:2@C8 106412 0.94 5.31 0.658 79 :1@N1_:2@N6 106276 0.939 4.98 0.82 80 :1@N7_:2@N3 104796 0.926 5.67 0.844 81 :1@N9_:2@N6 102544 0.906 5.93 0.619 82 :1@N7_:2@C2 99190 0.876 5.69 0.906 83 :1@C2_:2@N6 98073 0.866 5.63 0.696 84 :1@N3_:2@N6 97563 0.862 5.96 0.564 85 :1@C8_:2@N3 85888 0.759 5.98 0.784 86 :1@C8_:2@N1 83191 0.735 5.89 0.868 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 113220, 'v_base2' size 113220, output size 113220 TIME: Analyses took 0.0101 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 113220 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 113220 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 113220 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 113220 COM "COM" (double, distance), size is 113220 v_base1 "v_base1" (vector, vector), size is 113220 v_base2 "v_base2" (vector, vector), size is 113220 normalangle "normalangle" (double), size is 113220 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.15%) TIME: Trajectory Process : 1.3479 s ( 99.09%) TIME: Action Post : 0.0002 s ( 0.02%) TIME: Analysis : 0.0101 s ( 0.74%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.3602 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: 1.6582 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.