CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:31:51 | Available memory: 8386.75 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] 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*), with fitting. [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_00001 Saving minimum observed distances in set 'Contacts_00001[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: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 84566 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 84566 of 84566) Coordinate processing will occur on 84566 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 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] Vector 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] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c0 (1-84566, 1) ----- 0% 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 100 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@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@N3' 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@C2' Atom ':1@N1' to ':2@N3' 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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 84566 frames and processed 84566 frames. TIME: Trajectory processing: 7.1830 s TIME: Avg. throughput= 11773.0671 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 96.8336 100 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 84554 1 4.22 0.517 2 :1@C4_:2@C4 84550 1 4.32 0.461 3 :1@N9_:2@C5 84517 0.999 4.47 0.627 4 :1@C4_:2@C6 84512 0.999 4.44 0.538 5 :1@N3_:2@C4 84416 0.998 4.3 0.489 6 :1@N9_:2@C4 84402 0.998 4.86 0.609 7 :1@C5_:2@C6 84394 0.998 4.08 0.606 8 :1@C5_:2@C5 84382 0.998 4.25 0.636 9 :1@C4_:2@N9 84360 0.998 4.66 0.513 10 :1@C4_:2@N3 84340 0.997 4.64 0.651 11 :1@N3_:2@C5 84336 0.997 4.51 0.596 12 :1@C5_:2@N1 84322 0.997 4.15 0.649 13 :1@C4_:2@N1 84304 0.997 4.72 0.647 14 :1@N3_:2@N9 84289 0.997 4.4 0.506 15 :1@N3_:2@N3 84281 0.997 4.56 0.611 16 :1@C5_:2@C4 84266 0.996 4.43 0.581 17 :1@C2_:2@C4 84197 0.996 4.3 0.621 18 :1@N9_:2@N9 84193 0.996 5.11 0.62 19 :1@N9_:2@C6 84191 0.996 4.68 0.654 20 :1@C6_:2@C2 84189 0.996 3.98 0.611 21 :1@C2_:2@N3 84128 0.995 4.24 0.617 22 :1@N1_:2@N3 84086 0.994 4.09 0.55 23 :1@C5_:2@C2 84063 0.994 4.3 0.753 24 :1@N3_:2@C2 84040 0.994 4.96 0.72 25 :1@C6_:2@N1 84036 0.994 4.06 0.615 26 :1@N3_:2@C6 84021 0.994 4.97 0.652 27 :1@C4_:2@C2 84003 0.993 4.75 0.733 28 :1@N1_:2@C4 83994 0.993 4.41 0.607 29 :1@N1_:2@C2 83984 0.993 4.15 0.646 30 :1@C6_:2@N3 83936 0.993 4.2 0.582 31 :1@C2_:2@C2 83932 0.993 4.6 0.729 32 :1@C5_:2@N3 83896 0.992 4.5 0.706 33 :1@N7_:2@C6 83869 0.992 4.14 0.799 34 :1@C6_:2@C4 83859 0.992 4.45 0.548 35 :1@N3_:2@N1 83859 0.992 5.19 0.709 36 :1@C4_:2@N7 83831 0.991 4.5 0.746 37 :1@C4_:2@N6 83800 0.991 4.91 0.634 38 :1@C4_:2@C8 83779 0.991 4.73 0.708 39 :1@C2_:2@N9 83771 0.991 4.54 0.599 40 :1@N7_:2@C5 83686 0.99 4.52 0.796 41 :1@N3_:2@C8 83685 0.99 4.66 0.696 42 :1@N6_:2@C2 83604 0.989 4.06 0.694 43 :1@C8_:2@C5 83604 0.989 4.6 0.809 44 :1@C2_:2@C5 83582 0.988 4.72 0.762 45 :1@N3_:2@N7 83494 0.987 4.75 0.733 46 :1@C6_:2@C6 83436 0.987 4.3 0.696 47 :1@C6_:2@C5 83415 0.986 4.54 0.696 48 :1@C5_:2@N6 83388 0.986 4.43 0.697 49 :1@N6_:2@N1 83364 0.986 4.08 0.69 50 :1@N1_:2@N1 83281 0.985 4.52 0.758 51 :1@C5_:2@N9 83148 0.983 5.07 0.583 52 :1@C8_:2@C6 83095 0.983 4.44 0.806 53 :1@N7_:2@N1 83033 0.982 4.3 0.872 54 :1@N9_:2@N6 83027 0.982 4.88 0.691 55 :1@C2_:2@N1 82986 0.981 5.01 0.794 56 :1@N6_:2@N3 82951 0.981 4.56 0.659 57 :1@N1_:2@N9 82879 0.98 4.95 0.573 58 :1@N7_:2@N6 82838 0.98 4.11 0.807 59 :1@N1_:2@C5 82728 0.978 4.76 0.784 60 :1@N9_:2@N7 82704 0.978 4.44 0.753 61 :1@C6_:2@N9 82574 0.976 5.18 0.551 62 :1@C2_:2@C8 82478 0.975 5.08 0.75 63 :1@C2_:2@C6 82469 0.975 5.04 0.803 64 :1@N7_:2@C4 82426 0.975 4.99 0.746 65 :1@C5_:2@N7 82378 0.974 4.79 0.786 66 :1@N6_:2@C4 82252 0.973 5.03 0.605 67 :1@N9_:2@C8 82238 0.972 4.82 0.727 68 :1@N1_:2@C6 82215 0.972 4.77 0.824 69 :1@C8_:2@N6 82191 0.972 4.37 0.813 70 :1@C8_:2@C4 82036 0.97 5.16 0.75 71 :1@N6_:2@C6 81872 0.968 4.55 0.773 72 :1@C5_:2@C8 81495 0.964 5.22 0.705 73 :1@C2_:2@N7 81156 0.96 5.19 0.811 74 :1@C6_:2@N6 81137 0.959 4.79 0.809 75 :1@N9_:2@N1 80988 0.958 5.12 0.725 76 :1@N9_:2@N3 80937 0.957 5.32 0.745 77 :1@C8_:2@N7 80792 0.955 4.7 0.859 78 :1@N6_:2@C5 80596 0.953 5.05 0.722 79 :1@N7_:2@C2 80566 0.953 4.71 0.915 80 :1@N7_:2@N7 80382 0.951 4.95 0.849 81 :1@N3_:2@N6 80348 0.95 5.6 0.694 82 :1@C8_:2@N1 79919 0.945 4.81 0.845 83 :1@N7_:2@N3 79574 0.941 5.1 0.832 84 :1@C6_:2@N7 79540 0.941 5.26 0.78 85 :1@N1_:2@C8 79311 0.938 5.52 0.728 86 :1@N6_:2@N6 78863 0.933 4.9 0.918 87 :1@C6_:2@C8 78662 0.93 5.57 0.669 88 :1@C8_:2@N9 78587 0.929 5.61 0.692 89 :1@N1_:2@N7 78417 0.927 5.44 0.835 90 :1@C8_:2@C8 78168 0.924 5.31 0.765 91 :1@N7_:2@N9 77944 0.922 5.64 0.673 92 :1@N9_:2@C2 77696 0.919 5.31 0.79 93 :1@N6_:2@N9 76494 0.905 5.87 0.552 94 :1@N7_:2@C8 75489 0.893 5.54 0.713 95 :1@N1_:2@N6 75432 0.892 5.38 0.873 96 :1@C8_:2@N3 74846 0.885 5.43 0.78 97 :1@C8_:2@C2 74820 0.885 5.18 0.853 98 :1@C2_:2@N6 72180 0.854 5.65 0.792 99 :1@N6_:2@N7 69281 0.819 5.82 0.756 100 :1@N6_:2@C8 60274 0.713 6.13 0.585 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0073 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 84566 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 84566 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 84566 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 84566 COM "COM" (double, distance), size is 84566 v_base1 "v_base1" (vector), size is 84566 v_base2 "v_base2" (vector), size is 84566 normalangle "normalangle" (double), size is 84566 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 7.4184 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.