CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:18:17 | Available memory: 1.728 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 113822 of 113822) Coordinate processing will occur on 113822 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 (1-113822, 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 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 113822 frames and processed 113822 frames. TIME: Avg. throughput= 85753.8286 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 68.358 75 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 113411 0.996 4.4 0.494 2 :1@N9_:2@N7 113380 0.996 4.72 0.706 3 :1@N9_:2@N9 113357 0.996 5.27 0.528 4 :1@C4_:2@C5 113100 0.994 4.5 0.564 5 :1@N9_:2@C4 112905 0.992 4.74 0.477 6 :1@N9_:2@C8 112858 0.992 5.17 0.702 7 :1@C4_:2@N6 112585 0.989 4.23 0.657 8 :1@C4_:2@C6 112562 0.989 4.2 0.598 9 :1@N9_:2@C6 112529 0.989 4.35 0.578 10 :1@C8_:2@C5 112507 0.988 4.58 0.642 11 :1@C5_:2@N6 112496 0.988 3.93 0.648 12 :1@C5_:2@C5 112489 0.988 4.75 0.641 13 :1@C4_:2@C4 112407 0.988 5.02 0.579 14 :1@C5_:2@C6 112299 0.987 4.19 0.618 15 :1@N9_:2@N6 112248 0.986 4.6 0.675 16 :1@N7_:2@N6 111953 0.984 4.13 0.785 17 :1@C4_:2@N7 111951 0.984 4.85 0.746 18 :1@N7_:2@C5 111892 0.983 4.83 0.674 19 :1@C8_:2@C6 111838 0.983 4.37 0.684 20 :1@N7_:2@C6 111709 0.981 4.33 0.658 21 :1@C8_:2@N6 111644 0.981 4.48 0.828 22 :1@C6_:2@N6 111494 0.98 4.05 0.776 23 :1@N3_:2@C5 111195 0.977 4.82 0.714 24 :1@C8_:2@N7 111105 0.976 4.88 0.906 25 :1@N3_:2@C6 111101 0.976 4.56 0.783 26 :1@N9_:2@N3 110969 0.975 5.01 0.653 27 :1@C4_:2@N1 110865 0.974 4.43 0.806 28 :1@N9_:2@N1 110782 0.973 4.59 0.757 29 :1@N3_:2@N6 110700 0.973 4.6 0.836 30 :1@C6_:2@C6 110688 0.972 4.55 0.764 31 :1@C5_:2@N1 110425 0.97 4.39 0.812 32 :1@C5_:2@C4 110321 0.969 5.43 0.649 33 :1@N6_:2@N6 110304 0.969 4.38 0.852 34 :1@C5_:2@N7 110077 0.967 5.14 0.798 35 :1@C4_:2@N9 109817 0.965 5.65 0.587 36 :1@N9_:2@C2 109769 0.964 4.86 0.794 37 :1@C8_:2@N1 109335 0.961 4.57 0.871 38 :1@N7_:2@N1 109222 0.96 4.5 0.856 39 :1@N3_:2@C4 109169 0.959 5.27 0.691 40 :1@C4_:2@N3 108754 0.955 5.24 0.702 41 :1@C4_:2@C8 108513 0.953 5.46 0.723 42 :1@N1_:2@N6 108410 0.952 4.35 0.877 43 :1@C4_:2@C2 108275 0.951 4.88 0.838 44 :1@N7_:2@N7 108197 0.951 5.16 0.892 45 :1@C6_:2@C5 107748 0.947 5.27 0.712 46 :1@C2_:2@N6 107681 0.946 4.54 0.915 47 :1@N3_:2@N7 107296 0.943 5.06 0.867 48 :1@N6_:2@C6 107009 0.94 5.06 0.795 49 :1@C6_:2@N1 106952 0.94 4.67 0.878 50 :1@C2_:2@C6 106882 0.939 4.75 0.835 51 :1@N3_:2@N1 106513 0.936 4.68 0.938 52 :1@N1_:2@C6 106404 0.935 4.79 0.803 53 :1@C2_:2@C5 105239 0.925 5.22 0.766 54 :1@N1_:2@N1 102823 0.903 4.87 0.967 55 :1@C2_:2@N1 102545 0.901 4.81 1.03 56 :1@N3_:2@N9 102063 0.897 5.8 0.628 57 :1@N1_:2@C5 101890 0.895 5.45 0.721 58 :1@N3_:2@N3 101831 0.895 5.38 0.845 59 :1@N3_:2@C2 101590 0.893 5.01 1 60 :1@N3_:2@C8 100618 0.884 5.58 0.801 61 :1@C6_:2@N7 100591 0.884 5.61 0.782 62 :1@C5_:2@C8 97613 0.858 5.83 0.71 63 :1@C2_:2@N7 96789 0.85 5.41 0.913 64 :1@C2_:2@C4 94899 0.834 5.72 0.665 65 :1@N1_:2@N7 91757 0.806 5.7 0.834 66 :1@C2_:2@C2 90476 0.795 5.18 1.03 67 :1@N1_:2@C2 88584 0.778 5.43 0.903 68 :1@N1_:2@C4 82820 0.728 6 0.558 69 :1@C2_:2@N3 82792 0.727 5.67 0.801 70 :1@N6_:2@N7 76720 0.674 6.05 0.701 71 :1@C2_:2@C8 75219 0.661 5.9 0.774 72 :1@C2_:2@N9 71502 0.628 6.2 0.576 73 :1@C6_:2@C8 66739 0.586 6.2 0.662 74 :1@N1_:2@C8 54689 0.48 6.16 0.706 75 :1@N1_:2@N9 42761 0.376 6.41 0.501 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 113822, 'v_base2' size 113822, output size 113822 TIME: Analyses took 0.0100 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 113822 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 113822 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 113822 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 113822 COM "COM" (double, distance), size is 113822 v_base1 "v_base1" (vector, vector), size is 113822 v_base2 "v_base2" (vector, vector), size is 113822 normalangle "normalangle" (double), size is 113822 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0021 s ( 0.15%) TIME: Trajectory Process : 1.3273 s ( 99.08%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0100 s ( 0.74%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1.3396 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: 1.6605 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.