CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 13:17:46 | Available memory: 1.657 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 162772 of 162772) Coordinate processing will occur on 162772 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 (1-162772, 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 162772 frames and processed 162772 frames. TIME: Avg. throughput= 85852.9731 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 79.1168 90 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 159955 0.983 4.64 0.653 2 :1@C4_:2@C5 159640 0.981 4.65 0.64 3 :1@N9_:2@N7 159547 0.98 4.96 0.821 4 :1@C4_:2@C6 158661 0.975 4.34 0.66 5 :1@N9_:2@C4 158643 0.975 4.92 0.584 6 :1@C4_:2@N6 158572 0.974 4.38 0.727 7 :1@N9_:2@C6 158452 0.973 4.57 0.695 8 :1@C4_:2@N7 158093 0.971 5.01 0.804 9 :1@N3_:2@C5 157860 0.97 4.77 0.712 10 :1@N9_:2@N9 157656 0.969 5.42 0.596 11 :1@C4_:2@C4 157561 0.968 5.12 0.608 12 :1@N9_:2@C8 157521 0.968 5.37 0.773 13 :1@N3_:2@C6 157238 0.966 4.48 0.786 14 :1@N9_:2@N6 157168 0.966 4.82 0.773 15 :1@N3_:2@N6 156965 0.964 4.49 0.85 16 :1@C5_:2@C6 156773 0.963 4.45 0.799 17 :1@C5_:2@N6 156409 0.961 4.24 0.887 18 :1@C4_:2@N1 155922 0.958 4.52 0.808 19 :1@C5_:2@C5 155462 0.955 4.98 0.766 20 :1@N9_:2@N1 155414 0.955 4.76 0.787 21 :1@C6_:2@N6 154950 0.952 4.28 0.907 22 :1@N9_:2@N3 154789 0.951 5.13 0.682 23 :1@N3_:2@C4 154249 0.948 5.24 0.675 24 :1@N3_:2@N7 154101 0.947 5.04 0.847 25 :1@C6_:2@C6 153846 0.945 4.74 0.821 26 :1@C5_:2@N1 153525 0.943 4.57 0.879 27 :1@N9_:2@C2 153364 0.942 4.98 0.8 28 :1@C2_:2@N6 153060 0.94 4.38 0.944 29 :1@C8_:2@C5 152945 0.94 4.9 0.873 30 :1@C8_:2@C6 152703 0.938 4.7 0.919 31 :1@N1_:2@N6 152581 0.937 4.37 0.884 32 :1@C4_:2@C2 152032 0.934 4.94 0.835 33 :1@C2_:2@C6 151879 0.933 4.63 0.839 34 :1@C4_:2@N3 151739 0.932 5.3 0.704 35 :1@C4_:2@N9 151656 0.932 5.73 0.595 36 :1@C8_:2@C4 151142 0.929 5.25 0.741 37 :1@N3_:2@N1 151042 0.928 4.61 0.914 38 :1@C4_:2@C8 150875 0.927 5.58 0.75 39 :1@C2_:2@C5 150174 0.923 5.15 0.753 40 :1@N7_:2@C6 150097 0.922 4.65 0.911 41 :1@N1_:2@C6 150070 0.922 4.81 0.781 42 :1@C5_:2@C4 149769 0.92 5.56 0.671 43 :1@C8_:2@N1 149173 0.916 4.82 0.963 44 :1@C6_:2@N1 148869 0.915 4.79 0.896 45 :1@N6_:2@N6 148224 0.911 4.64 0.977 46 :1@N7_:2@N6 147419 0.906 4.47 1.03 47 :1@N7_:2@N1 147369 0.905 4.75 0.962 48 :1@C8_:2@N6 147299 0.905 4.76 0.994 49 :1@C6_:2@C5 146994 0.903 5.41 0.739 50 :1@C5_:2@C2 146299 0.899 5.12 0.856 51 :1@C2_:2@N1 146027 0.897 4.71 0.998 52 :1@N7_:2@C5 146024 0.897 5.07 0.832 53 :1@N1_:2@N1 145354 0.893 4.87 0.927 54 :1@N3_:2@N9 145310 0.893 5.8 0.625 55 :1@C8_:2@N3 145306 0.893 5.36 0.813 56 :1@N3_:2@C8 145277 0.893 5.59 0.788 57 :1@C5_:2@N7 145232 0.892 5.3 0.856 58 :1@C8_:2@C2 145201 0.892 5.08 0.95 59 :1@N3_:2@C2 145024 0.891 4.99 0.961 60 :1@N3_:2@N3 145014 0.891 5.38 0.812 61 :1@N1_:2@C5 143630 0.882 5.49 0.701 62 :1@C8_:2@N7 143165 0.88 5.11 1 63 :1@N6_:2@C6 142850 0.878 5.24 0.841 64 :1@N7_:2@C4 141565 0.87 5.6 0.721 65 :1@C8_:2@N9 141434 0.869 5.74 0.712 66 :1@C2_:2@N7 140796 0.865 5.39 0.884 67 :1@C5_:2@N3 140486 0.863 5.64 0.71 68 :1@N7_:2@C2 139773 0.859 5.19 0.942 69 :1@N6_:2@N1 137674 0.846 5.23 0.874 70 :1@C2_:2@C4 137116 0.842 5.69 0.649 71 :1@C6_:2@C2 134494 0.826 5.43 0.832 72 :1@N7_:2@N3 133338 0.819 5.64 0.796 73 :1@C8_:2@C8 133084 0.818 5.54 0.869 74 :1@N7_:2@N7 132564 0.814 5.3 0.943 75 :1@C2_:2@C2 131965 0.811 5.18 0.987 76 :1@C6_:2@N7 129384 0.795 5.68 0.789 77 :1@N1_:2@N7 126934 0.78 5.74 0.818 78 :1@C6_:2@C4 124558 0.765 5.99 0.595 79 :1@C5_:2@C8 121576 0.747 5.89 0.723 80 :1@C2_:2@N3 121375 0.746 5.69 0.769 81 :1@C5_:2@N9 121310 0.745 6.13 0.597 82 :1@N1_:2@C4 118273 0.727 6.04 0.546 83 :1@N6_:2@C5 118234 0.726 5.9 0.681 84 :1@C2_:2@C8 111131 0.683 5.93 0.761 85 :1@N7_:2@N9 111049 0.682 6.09 0.663 86 :1@N7_:2@C8 109064 0.67 5.81 0.777 87 :1@C2_:2@N9 105028 0.645 6.21 0.571 88 :1@N6_:2@N7 91659 0.563 6.06 0.7 89 :1@C6_:2@C8 81913 0.503 6.2 0.664 90 :1@N1_:2@C8 73058 0.449 6.17 0.695 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 162772, 'v_base2' size 162772, output size 162772 TIME: Analyses took 0.0140 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 162772 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 162772 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 162772 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 162772 COM "COM" (double, distance), size is 162772 v_base1 "v_base1" (vector, vector), size is 162772 v_base2 "v_base2" (vector, vector), size is 162772 normalangle "normalangle" (double), size is 162772 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.10%) TIME: Trajectory Process : 1.8959 s ( 99.15%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0140 s ( 0.73%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1.9123 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: 2.3658 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.