CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 17:30:12 | Available memory: 53911.1 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.c1] Reading '../ctraj.c1' 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, 129043 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 129043 of 129043) Coordinate processing will occur on 129043 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.c1 (1-129043, 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 129043 frames and processed 129043 frames. TIME: Trajectory processing: 0.7827 s TIME: Avg. throughput= 164862.5134 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 96.0418 100 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 128923 0.999 4.6 0.506 2 :1@N3_:2@N9 128866 0.999 4.35 0.52 3 :1@C2_:2@N9 128428 0.995 4.49 0.606 4 :1@C5_:2@N9 128315 0.994 5.01 0.584 5 :1@N9_:2@N9 128298 0.994 5.06 0.605 6 :1@C4_:2@C8 128145 0.993 4.58 0.693 7 :1@N1_:2@N9 128108 0.993 4.9 0.597 8 :1@C6_:2@N9 128028 0.992 5.14 0.573 9 :1@N3_:2@C8 127912 0.991 4.54 0.714 10 :1@N9_:2@C8 127910 0.991 4.69 0.691 11 :1@C5_:2@C4 127824 0.991 4.4 0.581 12 :1@C4_:2@C4 127630 0.989 4.33 0.508 13 :1@C6_:2@N3 127588 0.989 4.22 0.59 14 :1@C6_:2@C4 127441 0.988 4.41 0.53 15 :1@N6_:2@N3 127296 0.986 4.55 0.665 16 :1@C5_:2@N3 127226 0.986 4.57 0.744 17 :1@N1_:2@N3 127225 0.986 4.08 0.543 18 :1@N3_:2@C4 127081 0.985 4.3 0.519 19 :1@C4_:2@N3 126924 0.984 4.74 0.688 20 :1@N1_:2@C4 126918 0.984 4.35 0.584 21 :1@C2_:2@C4 126868 0.983 4.28 0.613 22 :1@C2_:2@N3 126855 0.983 4.28 0.643 23 :1@N9_:2@N7 126854 0.983 4.28 0.67 24 :1@N3_:2@N3 126767 0.982 4.66 0.644 25 :1@N9_:2@C4 126763 0.982 4.87 0.651 26 :1@C6_:2@C2 126740 0.982 4 0.62 27 :1@N6_:2@C2 126732 0.982 4.03 0.662 28 :1@C5_:2@C5 126375 0.979 4.12 0.577 29 :1@C5_:2@C2 126325 0.979 4.4 0.793 30 :1@N1_:2@C2 126321 0.979 4.17 0.666 31 :1@C4_:2@C5 126317 0.979 4.13 0.466 32 :1@C4_:2@N7 126300 0.979 4.32 0.701 33 :1@N7_:2@C5 126278 0.979 4.39 0.739 34 :1@N9_:2@C5 126274 0.979 4.39 0.565 35 :1@N6_:2@C4 126199 0.978 4.98 0.608 36 :1@C5_:2@C8 126120 0.977 5.08 0.738 37 :1@C5_:2@N1 126089 0.977 4.18 0.648 38 :1@N3_:2@C5 126061 0.977 4.48 0.578 39 :1@C8_:2@N7 126012 0.977 4.54 0.82 40 :1@C5_:2@C6 125953 0.976 4 0.524 41 :1@C2_:2@C8 125942 0.976 4.99 0.788 42 :1@C2_:2@C2 125928 0.976 4.69 0.755 43 :1@C6_:2@N1 125919 0.976 4.04 0.579 44 :1@C4_:2@C6 125918 0.976 4.42 0.522 45 :1@N7_:2@C6 125916 0.976 4.03 0.722 46 :1@C8_:2@C5 125876 0.975 4.48 0.742 47 :1@N7_:2@C4 125864 0.975 4.97 0.758 48 :1@C4_:2@N1 125792 0.975 4.82 0.687 49 :1@N3_:2@N7 125740 0.974 4.63 0.722 50 :1@C4_:2@C2 125637 0.974 4.9 0.765 51 :1@N3_:2@C2 125600 0.973 5.1 0.731 52 :1@N9_:2@C6 125577 0.973 4.67 0.658 53 :1@N3_:2@C6 125486 0.972 5.02 0.635 54 :1@N6_:2@N1 125470 0.972 4 0.626 55 :1@N7_:2@N6 125392 0.972 3.97 0.695 56 :1@C2_:2@C5 125363 0.971 4.69 0.75 57 :1@C6_:2@C5 125358 0.971 4.42 0.68 58 :1@C4_:2@N6 125230 0.97 4.87 0.591 59 :1@N9_:2@N6 125114 0.97 4.85 0.647 60 :1@C6_:2@C6 125105 0.969 4.22 0.66 61 :1@N3_:2@N1 125068 0.969 5.32 0.703 62 :1@N7_:2@N1 124986 0.969 4.34 0.895 63 :1@C8_:2@N6 124967 0.968 4.28 0.735 64 :1@N1_:2@N1 124961 0.968 4.54 0.747 65 :1@C8_:2@C6 124945 0.968 4.39 0.781 66 :1@C5_:2@N6 124922 0.968 4.32 0.624 67 :1@C5_:2@N7 124855 0.968 4.59 0.804 68 :1@N1_:2@C5 124504 0.965 4.7 0.781 69 :1@C8_:2@C8 124375 0.964 5.21 0.765 70 :1@N7_:2@N7 124307 0.963 4.76 0.842 71 :1@C2_:2@N1 124243 0.963 5.1 0.766 72 :1@C8_:2@C4 124084 0.962 5.16 0.763 73 :1@N6_:2@C6 123684 0.958 4.44 0.764 74 :1@C2_:2@C6 123626 0.958 5.08 0.763 75 :1@N1_:2@C6 123574 0.958 4.76 0.806 76 :1@C2_:2@N7 122959 0.953 5.11 0.84 77 :1@N6_:2@C5 122871 0.952 4.95 0.74 78 :1@C8_:2@N9 122621 0.95 5.58 0.678 79 :1@C6_:2@N6 122389 0.948 4.71 0.811 80 :1@N1_:2@C8 122049 0.946 5.44 0.769 81 :1@C6_:2@C8 121734 0.943 5.47 0.729 82 :1@N7_:2@N9 121574 0.942 5.61 0.655 83 :1@C6_:2@N7 121248 0.94 5.13 0.848 84 :1@N7_:2@C2 120918 0.937 4.81 0.961 85 :1@N3_:2@N6 120650 0.935 5.65 0.646 86 :1@N7_:2@N3 120395 0.933 5.19 0.875 87 :1@N7_:2@C8 120128 0.931 5.43 0.729 88 :1@N6_:2@N6 119769 0.928 4.79 0.944 89 :1@N1_:2@N7 119493 0.926 5.36 0.875 90 :1@N9_:2@N1 119120 0.923 5.23 0.769 91 :1@N9_:2@N3 119025 0.922 5.43 0.746 92 :1@N6_:2@N9 119005 0.922 5.84 0.559 93 :1@C8_:2@N1 118725 0.92 4.88 0.886 94 :1@N1_:2@N6 113956 0.883 5.4 0.836 95 :1@N9_:2@C2 111633 0.865 5.44 0.759 96 :1@C8_:2@N3 109716 0.85 5.52 0.793 97 :1@C8_:2@C2 108756 0.843 5.29 0.857 98 :1@C2_:2@N6 108663 0.842 5.72 0.701 99 :1@N6_:2@N7 107802 0.835 5.72 0.807 100 :1@N6_:2@C8 94708 0.734 6.06 0.603 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0066 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 129043 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 129043 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 129043 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 129043 COM "COM" (double, distance), size is 129043 v_base1 "v_base1" (vector), size is 129043 v_base2 "v_base2" (vector), size is 129043 normalangle "normalangle" (double), size is 129043 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: 1.0184 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.