CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 13:09:25 | Available memory: 1.219 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,C6,C5,C4,O4,N3,C2,O2', 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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [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] [vector v_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] [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, 63 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 25808 of 25808) Coordinate processing will occur on 25808 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*](40) Reference mask: [:1,2&!@H*](40) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [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. 6: [vector v_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-25808, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 82 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@O4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@O4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@O4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C4' Atom ':1@O6' to ':2@O4' Atom ':1@O6' to ':2@N3' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C4' Atom ':1@N2' to ':2@O4' Atom ':1@N2' to ':2@N3' Atom ':1@N2' to ':2@C2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 25808 frames and processed 25808 frames. TIME: Avg. throughput= 116844.8980 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 72.2309 82 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C6 25664 0.994 4.84 0.609 2 :1@C4_:2@C5 25657 0.994 4.27 0.724 3 :1@N9_:2@C5 25643 0.994 4.53 0.668 4 :1@C4_:2@C6 25529 0.989 4.71 0.693 5 :1@C4_:2@C4 25485 0.987 4.43 0.717 6 :1@N3_:2@C5 25439 0.986 4.25 0.788 7 :1@N9_:2@C4 25346 0.982 4.78 0.72 8 :1@C4_:2@O4 25298 0.98 4.58 0.772 9 :1@N3_:2@C6 25279 0.98 4.57 0.781 10 :1@N3_:2@C4 25149 0.974 4.57 0.797 11 :1@C5_:2@C4 25108 0.973 4.39 0.836 12 :1@N9_:2@N1 25031 0.97 5.32 0.618 13 :1@C5_:2@C5 25007 0.969 4.56 0.795 14 :1@C5_:2@O4 24993 0.968 4.28 0.918 15 :1@N9_:2@O4 24813 0.961 5 0.77 16 :1@C2_:2@C5 24810 0.961 4.5 0.928 17 :1@C4_:2@N3 24767 0.96 4.89 0.773 18 :1@N3_:2@O4 24737 0.959 4.79 0.834 19 :1@C4_:2@N1 24715 0.958 5.19 0.662 20 :1@C6_:2@O4 24597 0.953 4.23 1.05 21 :1@C8_:2@C5 24563 0.952 4.88 0.795 22 :1@C6_:2@C4 24483 0.949 4.51 0.944 23 :1@N9_:2@N3 24424 0.946 5.18 0.801 24 :1@C2_:2@C6 24250 0.94 4.93 0.879 25 :1@N3_:2@N1 24219 0.938 5.08 0.83 26 :1@C8_:2@C4 24206 0.938 4.83 0.885 27 :1@C5_:2@N3 24201 0.938 4.79 0.862 28 :1@C8_:2@C6 24164 0.936 5.32 0.69 29 :1@N1_:2@C5 24153 0.936 4.78 0.926 30 :1@C5_:2@C6 24080 0.933 5.14 0.668 31 :1@C2_:2@C4 24005 0.93 4.53 0.915 32 :1@C4_:2@C2 23992 0.93 5.25 0.745 33 :1@N7_:2@C5 23900 0.926 4.91 0.738 34 :1@N7_:2@C4 23899 0.926 4.63 0.815 35 :1@N9_:2@C2 23893 0.926 5.44 0.763 36 :1@C6_:2@C5 23890 0.926 4.83 0.809 37 :1@N1_:2@C4 23800 0.922 4.52 0.969 38 :1@N3_:2@N3 23789 0.922 4.98 0.808 39 :1@N1_:2@O4 23753 0.92 4.34 1.05 40 :1@N7_:2@O4 23677 0.917 4.45 0.914 41 :1@C2_:2@O4 23497 0.91 4.55 0.947 42 :1@C8_:2@O4 23433 0.908 4.82 0.947 43 :1@N7_:2@N3 23316 0.903 4.99 0.937 44 :1@O6_:2@O4 23299 0.903 4.4 1.03 45 :1@N7_:2@C6 23129 0.896 5.51 0.658 46 :1@N2_:2@C5 23032 0.892 4.8 0.909 47 :1@C8_:2@N3 22982 0.89 5.13 0.952 48 :1@C5_:2@N1 22929 0.888 5.51 0.711 49 :1@N3_:2@C2 22890 0.887 5.21 0.836 50 :1@C5_:2@C2 22742 0.881 5.31 0.829 51 :1@C6_:2@N3 22670 0.878 4.78 0.883 52 :1@N2_:2@C6 22652 0.878 5.17 0.924 53 :1@O6_:2@C4 22637 0.877 4.84 0.847 54 :1@C2_:2@N3 22459 0.87 4.86 0.963 55 :1@C8_:2@N1 22393 0.868 5.61 0.754 56 :1@N1_:2@C6 22388 0.867 5.33 0.768 57 :1@C6_:2@C6 22372 0.867 5.49 0.664 58 :1@N1_:2@N3 22092 0.856 4.79 0.978 59 :1@O6_:2@C5 21961 0.851 5.41 0.699 60 :1@C2_:2@N1 21894 0.848 5.22 0.989 61 :1@N2_:2@C4 21780 0.844 4.85 0.907 62 :1@N7_:2@C2 21284 0.825 5.49 0.915 63 :1@N7_:2@N1 21179 0.821 5.77 0.761 64 :1@O6_:2@N3 21095 0.817 5.05 0.855 65 :1@C2_:2@C2 21037 0.815 5.16 1.07 66 :1@C8_:2@C2 20981 0.813 5.42 0.873 67 :1@N2_:2@O4 20817 0.807 4.84 0.936 68 :1@C6_:2@C2 20649 0.8 5.35 0.855 69 :1@N2_:2@N3 20119 0.78 5.13 1.12 70 :1@C4_:2@O2 20094 0.779 5.76 0.784 71 :1@N1_:2@C2 19994 0.775 5.23 1.02 72 :1@C6_:2@N1 19847 0.769 5.68 0.706 73 :1@N1_:2@N1 19696 0.763 5.49 0.865 74 :1@N2_:2@N1 19240 0.746 5.27 1.2 75 :1@C5_:2@O2 18752 0.727 5.69 0.9 76 :1@O6_:2@C6 18406 0.713 6.08 0.572 77 :1@N3_:2@O2 18152 0.703 5.64 0.84 78 :1@N9_:2@O2 17967 0.696 5.8 0.8 79 :1@N2_:2@C2 17306 0.671 5.1 1.29 80 :1@C8_:2@O2 16011 0.62 5.59 0.862 81 :1@N7_:2@O2 15294 0.593 5.56 0.933 82 :1@C2_:2@O2 15261 0.591 5.23 1.03 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 25808, 'v_base2' size 25808, output size 25808 TIME: Analyses took 0.0019 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 25808 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 25808 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 25808 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 25808 COM "COM" (double, distance), size is 25808 v_base2 "v_base2" (vector, vector), size is 25808 v_base1 "v_base1" (vector, vector), size is 25808 normalangle "normalangle" (double), size is 25808 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.2209 s ( 99.04%) TIME: Action Post : 0.0002 s ( 0.07%) TIME: Analysis : 0.0019 s ( 0.86%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2230 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: 0.2969 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.