CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:16:09 | Available memory: 52176.7 MB INPUT: Reading Input from file 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-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c3] Reading '../ctraj.c3' 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] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 79302 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 79302 of 79302) Coordinate processing will occur on 79302 frames. TIME: Run Initialization took 0.0006 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: 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] 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.c3 (1-79302, 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 79302 frames and processed 79302 frames. TIME: Trajectory processing: 0.5027 s TIME: Avg. throughput= 157747.1177 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 78.0269 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 76371 0.963 5.18 0.601 2 :1@C4_:2@C5 75960 0.958 4.97 0.673 3 :1@C4_:2@C6 75626 0.954 4.65 0.72 4 :1@C4_:2@N6 75222 0.949 4.74 0.759 5 :1@N9_:2@C6 75183 0.948 5.11 0.625 6 :1@N9_:2@N7 75146 0.948 5.53 0.722 7 :1@N3_:2@N6 75011 0.946 4.3 0.855 8 :1@N9_:2@C4 74715 0.942 5.29 0.623 9 :1@N3_:2@C5 74565 0.94 4.7 0.728 10 :1@N3_:2@C6 74367 0.938 4.32 0.805 11 :1@C4_:2@N7 74275 0.937 5.38 0.752 12 :1@C2_:2@N6 74052 0.934 4.04 0.904 13 :1@N3_:2@N7 73903 0.932 5.06 0.805 14 :1@C4_:2@N1 73804 0.931 4.69 0.825 15 :1@N9_:2@N6 73693 0.929 5.41 0.663 16 :1@C5_:2@C6 73376 0.925 4.92 0.88 17 :1@C4_:2@C4 73333 0.925 5.3 0.611 18 :1@N9_:2@C8 73152 0.922 5.83 0.692 19 :1@N9_:2@N9 73085 0.922 5.75 0.582 20 :1@N9_:2@N1 72843 0.919 5.12 0.748 21 :1@C2_:2@C6 72822 0.918 4.34 0.783 22 :1@N1_:2@N6 72652 0.916 4.29 0.878 23 :1@C5_:2@N6 72397 0.913 4.89 0.923 24 :1@N3_:2@N1 72346 0.912 4.48 0.893 25 :1@C2_:2@C5 72078 0.909 4.98 0.702 26 :1@N3_:2@C4 71924 0.907 5.19 0.627 27 :1@C5_:2@N1 71819 0.906 4.82 0.923 28 :1@C6_:2@N6 71556 0.902 4.66 0.978 29 :1@C2_:2@N1 71519 0.902 4.49 0.924 30 :1@N1_:2@C6 71262 0.899 4.71 0.704 31 :1@C6_:2@C6 71177 0.898 4.94 0.864 32 :1@C4_:2@C2 71168 0.897 4.97 0.846 33 :1@C5_:2@C5 70920 0.894 5.37 0.863 34 :1@N1_:2@N1 70637 0.891 4.74 0.813 35 :1@N9_:2@N3 70376 0.887 5.27 0.75 36 :1@N9_:2@C2 70305 0.887 5.14 0.828 37 :1@C2_:2@N7 70064 0.884 5.39 0.831 38 :1@C6_:2@N1 70014 0.883 4.84 0.887 39 :1@C4_:2@N3 69895 0.881 5.32 0.708 40 :1@N3_:2@C2 69699 0.879 4.93 0.878 41 :1@C4_:2@C8 69404 0.875 5.87 0.663 42 :1@N3_:2@C8 69291 0.874 5.67 0.694 43 :1@N3_:2@N3 68833 0.868 5.35 0.726 44 :1@C4_:2@N9 68553 0.864 5.89 0.514 45 :1@N1_:2@C5 68534 0.864 5.47 0.636 46 :1@C8_:2@C6 68526 0.864 5.46 0.86 47 :1@N3_:2@N9 68414 0.863 5.83 0.543 48 :1@C2_:2@C4 68265 0.861 5.63 0.58 49 :1@C2_:2@C2 68222 0.86 5.16 0.905 50 :1@C8_:2@C5 68089 0.859 5.57 0.932 51 :1@C5_:2@C2 66922 0.844 5.09 0.886 52 :1@C8_:2@N1 66576 0.84 5.32 0.881 53 :1@C8_:2@C4 66154 0.834 5.57 0.934 54 :1@C5_:2@C4 66058 0.833 5.67 0.764 55 :1@N1_:2@C2 65846 0.83 5.43 0.789 56 :1@C6_:2@C5 65747 0.829 5.57 0.79 57 :1@N7_:2@C6 65676 0.828 5.33 1.01 58 :1@N7_:2@N1 65210 0.822 5.15 0.985 59 :1@C8_:2@C2 64371 0.812 5.24 0.925 60 :1@N6_:2@N6 64358 0.812 5.06 1.06 61 :1@C6_:2@C2 63829 0.805 5.32 0.803 62 :1@C8_:2@N3 63632 0.802 5.41 0.911 63 :1@C2_:2@N3 63462 0.8 5.72 0.675 64 :1@N6_:2@N1 62805 0.792 5.25 0.924 65 :1@C5_:2@N3 62423 0.787 5.53 0.743 66 :1@N6_:2@C6 62143 0.784 5.42 0.95 67 :1@C8_:2@N6 61730 0.778 5.64 0.825 68 :1@N7_:2@N6 61617 0.777 5.37 0.966 69 :1@N1_:2@C4 61604 0.777 6.08 0.459 70 :1@N7_:2@C2 61153 0.771 5.18 0.969 71 :1@N1_:2@N7 59877 0.755 5.85 0.758 72 :1@C5_:2@N7 59754 0.753 5.66 0.901 73 :1@N7_:2@C5 59711 0.753 5.56 1.09 74 :1@N7_:2@N3 57531 0.725 5.51 0.959 75 :1@C6_:2@C4 57370 0.723 6.01 0.628 76 :1@C2_:2@C8 57020 0.719 6.05 0.677 77 :1@N1_:2@N3 56982 0.719 6.06 0.547 78 :1@N7_:2@C4 56796 0.716 5.68 1.07 79 :1@C6_:2@N3 55332 0.698 5.89 0.605 80 :1@C8_:2@N7 55151 0.695 5.71 1.01 81 :1@C8_:2@N9 55015 0.694 5.9 1 82 :1@C2_:2@N9 54461 0.687 6.27 0.476 83 :1@N6_:2@C2 53196 0.671 5.64 0.793 84 :1@C6_:2@N7 50724 0.64 5.8 0.812 85 :1@C5_:2@N9 48239 0.608 6.16 0.737 86 :1@C8_:2@C8 45514 0.574 5.82 1.07 87 :1@N6_:2@C5 44929 0.567 5.88 0.881 88 :1@N7_:2@N7 43630 0.55 5.6 1.16 89 :1@C5_:2@C8 42764 0.539 5.97 0.809 90 :1@N6_:2@N3 36219 0.457 6.14 0.659 91 :1@N7_:2@N9 34741 0.438 5.82 1.2 92 :1@N1_:2@C8 32264 0.407 6.3 0.582 93 :1@N7_:2@C8 29281 0.369 5.58 1.19 94 :1@N6_:2@N7 29023 0.366 5.84 0.863 95 :1@C6_:2@C8 28649 0.361 6.13 0.654 96 :1@N6_:2@C4 28408 0.358 6.13 0.79 97 :1@N1_:2@N9 26848 0.339 6.55 0.401 98 :1@C6_:2@N9 24759 0.312 6.3 0.597 99 :1@N6_:2@C8 13777 0.174 5.99 0.698 100 :1@N6_:2@N9 9968 0.126 5.95 0.525 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0039 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 79302 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 79302 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 79302 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 79302 COM "COM" (double, distance), size is 79302 v_base1 "v_base1" (vector), size is 79302 v_base2 "v_base2" (vector), size is 79302 normalangle "normalangle" (double), size is 79302 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: 0.6653 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.