CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 14:44:07 | Available memory: 1.727 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.c0] Reading '../ctraj.c0' 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,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6] 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,N2,H21,H22,N7,C8,H8,N9,O6, 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 148605 of 148605) Coordinate processing will occur on 148605 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*](42) Reference mask: [:1,2&!@H*](42) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6] :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,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c0 (1-148605, 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 97 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@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N2' 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@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N2' 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@O6' 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@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' Atom ':1@C6' to ':2@N3' 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@O6' Atom ':1@N6' to ':2@N1' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@O6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N2' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' 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@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' 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 148605 frames and processed 148605 frames. TIME: Avg. throughput= 81910.1059 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 85.2799 97 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 146314 0.985 4.78 0.708 2 :1@C4_:2@C5 145707 0.98 4.73 0.687 3 :1@N9_:2@C4 145472 0.979 4.92 0.585 4 :1@C4_:2@C6 145284 0.978 4.38 0.729 5 :1@N9_:2@C6 145020 0.976 4.72 0.757 6 :1@N9_:2@N9 144702 0.974 5.46 0.62 7 :1@C4_:2@O6 144351 0.971 4.56 0.83 8 :1@C4_:2@C4 144069 0.969 5.04 0.612 9 :1@N3_:2@C5 143476 0.965 4.72 0.732 10 :1@N9_:2@N7 143117 0.963 5.19 0.852 11 :1@N3_:2@C6 143038 0.963 4.33 0.808 12 :1@N9_:2@N1 142909 0.962 4.73 0.768 13 :1@N9_:2@N3 142495 0.959 4.98 0.634 14 :1@N3_:2@O6 142401 0.958 4.45 0.906 15 :1@C4_:2@N1 142371 0.958 4.34 0.744 16 :1@C5_:2@C6 142142 0.957 4.55 0.892 17 :1@N9_:2@C2 141602 0.953 4.84 0.757 18 :1@N9_:2@C8 141109 0.95 5.52 0.791 19 :1@C5_:2@N1 141049 0.949 4.48 0.849 20 :1@C4_:2@N7 140980 0.949 5.22 0.809 21 :1@N3_:2@C4 140767 0.947 5.07 0.654 22 :1@N9_:2@O6 140505 0.945 5.02 0.815 23 :1@C5_:2@C5 139945 0.942 5.09 0.84 24 :1@C5_:2@O6 139585 0.939 4.5 1.02 25 :1@N3_:2@N1 139499 0.939 4.27 0.85 26 :1@C4_:2@N3 139442 0.938 5.02 0.612 27 :1@C4_:2@C2 139439 0.938 4.63 0.706 28 :1@C4_:2@N9 139374 0.938 5.73 0.648 29 :1@C8_:2@C4 139035 0.936 5.31 0.781 30 :1@C6_:2@C6 138557 0.932 4.73 0.864 31 :1@C2_:2@C6 138295 0.931 4.42 0.824 32 :1@C6_:2@O6 138038 0.929 4.47 1.02 33 :1@C6_:2@N1 137934 0.928 4.59 0.81 34 :1@C8_:2@N1 137800 0.927 4.95 0.979 35 :1@N3_:2@N7 137669 0.926 5.16 0.798 36 :1@C5_:2@C4 137553 0.926 5.51 0.726 37 :1@C2_:2@N1 137529 0.925 4.35 0.909 38 :1@C8_:2@N3 137426 0.925 5.31 0.796 39 :1@C2_:2@O6 137345 0.924 4.27 0.961 40 :1@N3_:2@N3 137317 0.924 5.08 0.725 41 :1@N1_:2@N1 137202 0.923 4.57 0.82 42 :1@C8_:2@C5 136937 0.921 5.08 0.967 43 :1@C8_:2@C2 136900 0.921 5.09 0.935 44 :1@C8_:2@C6 136882 0.921 4.93 1.02 45 :1@N3_:2@C2 136856 0.921 4.63 0.845 46 :1@N1_:2@C6 136630 0.919 4.68 0.771 47 :1@C5_:2@C2 136458 0.918 4.87 0.771 48 :1@N1_:2@O6 136350 0.918 4.38 0.921 49 :1@N7_:2@N1 135856 0.914 4.84 1.01 50 :1@C2_:2@C5 134933 0.908 5.04 0.722 51 :1@N7_:2@C6 134229 0.903 4.85 1.06 52 :1@N3_:2@N9 133564 0.899 5.75 0.658 53 :1@C5_:2@N3 133400 0.898 5.41 0.689 54 :1@C4_:2@N2 133239 0.897 4.95 0.837 55 :1@C4_:2@C8 132853 0.894 5.7 0.761 56 :1@C2_:2@C2 132622 0.892 4.86 0.896 57 :1@C6_:2@C2 131945 0.888 5.15 0.79 58 :1@N9_:2@N2 131364 0.884 5.16 0.827 59 :1@N1_:2@C2 131263 0.883 5.18 0.85 60 :1@C2_:2@C4 131241 0.883 5.55 0.67 61 :1@N7_:2@C2 131126 0.882 5.11 0.922 62 :1@C6_:2@C5 130478 0.878 5.45 0.798 63 :1@N3_:2@C8 129875 0.874 5.68 0.766 64 :1@N6_:2@N1 129042 0.868 5.1 0.856 65 :1@N1_:2@C5 128967 0.868 5.44 0.709 66 :1@N7_:2@C4 128943 0.868 5.61 0.793 67 :1@N6_:2@O6 128233 0.863 4.82 1.08 68 :1@C2_:2@N3 127840 0.86 5.49 0.762 69 :1@C5_:2@N2 127464 0.858 5.02 0.871 70 :1@N3_:2@N2 127377 0.857 4.88 0.959 71 :1@N7_:2@C5 127312 0.857 5.2 0.941 72 :1@N7_:2@N3 127078 0.855 5.54 0.795 73 :1@N6_:2@C6 126955 0.854 5.24 0.904 74 :1@N7_:2@O6 125567 0.845 4.73 1.17 75 :1@C2_:2@N7 125446 0.844 5.51 0.84 76 :1@C8_:2@N9 125280 0.843 5.76 0.751 77 :1@C8_:2@O6 124336 0.837 4.98 1.07 78 :1@C6_:2@N2 121688 0.819 5.16 0.896 79 :1@C8_:2@N2 120636 0.812 5.21 1.04 80 :1@C6_:2@N3 120062 0.808 5.82 0.713 81 :1@C5_:2@N7 119984 0.807 5.43 0.86 82 :1@C2_:2@N2 119862 0.807 4.92 1 83 :1@C6_:2@C4 119747 0.806 5.93 0.71 84 :1@N1_:2@C4 119249 0.802 5.98 0.664 85 :1@N1_:2@N2 117588 0.791 5.14 0.962 86 :1@N1_:2@N3 116516 0.784 5.86 0.735 87 :1@C8_:2@N7 115641 0.778 5.19 0.998 88 :1@N1_:2@N7 108641 0.731 5.87 0.797 89 :1@C8_:2@C8 107886 0.726 5.57 0.854 90 :1@C5_:2@N9 107517 0.724 6.1 0.701 91 :1@N7_:2@N7 103246 0.695 5.31 0.906 92 :1@C6_:2@N7 102562 0.69 5.74 0.766 93 :1@N6_:2@C5 97850 0.658 5.86 0.75 94 :1@C5_:2@C8 96717 0.651 5.89 0.732 95 :1@N7_:2@N9 95223 0.641 6.03 0.736 96 :1@N7_:2@C8 87859 0.591 5.8 0.773 97 :1@N6_:2@N7 71837 0.483 6.08 0.679 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 148605, 'v_base2' size 148605, output size 148605 TIME: Analyses took 0.0128 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 148605 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 148605 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 148605 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 148605 COM "COM" (double, distance), size is 148605 v_base1 "v_base1" (vector, vector), size is 148605 v_base2 "v_base2" (vector, vector), size is 148605 normalangle "normalangle" (double), size is 148605 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.11%) TIME: Trajectory Process : 1.8142 s ( 99.18%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0128 s ( 0.70%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.8293 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: 2.2390 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.