CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 15:58:57 | Available memory: 55241.5 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.c2] Reading '../ctraj.c2' 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, 82883 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 82883 of 82883) Coordinate processing will occur on 82883 frames. TIME: Run Initialization took 0.0005 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.c2 (1-82883, 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 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@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@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@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@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 82883 frames and processed 82883 frames. TIME: Trajectory processing: 0.5030 s TIME: Avg. throughput= 164777.0084 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 78.1263 90 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 82674 0.997 4.87 0.618 2 :1@N9_:2@C4 82511 0.996 5.06 0.535 3 :1@C4_:2@C5 82444 0.995 4.78 0.623 4 :1@N9_:2@C6 82442 0.995 4.79 0.694 5 :1@N3_:2@N7 82089 0.99 4.86 0.775 6 :1@C4_:2@C6 81933 0.989 4.51 0.687 7 :1@C4_:2@N6 81919 0.988 4.58 0.754 8 :1@C4_:2@N7 81379 0.982 5.12 0.815 9 :1@C5_:2@C6 81276 0.981 4.71 0.833 10 :1@N9_:2@N9 81269 0.981 5.57 0.536 11 :1@C4_:2@C4 81077 0.978 5.23 0.604 12 :1@N9_:2@N6 81069 0.978 5.09 0.796 13 :1@N9_:2@N7 80965 0.977 5.25 0.815 14 :1@N9_:2@N3 80884 0.976 5.17 0.672 15 :1@N9_:2@N1 80883 0.976 4.87 0.769 16 :1@N3_:2@C5 80651 0.973 4.69 0.714 17 :1@C5_:2@N6 80332 0.969 4.59 0.966 18 :1@C5_:2@C5 79983 0.965 5.21 0.79 19 :1@C8_:2@N1 79959 0.965 4.87 0.988 20 :1@N3_:2@C8 79929 0.964 5.48 0.763 21 :1@N9_:2@C2 79792 0.963 5 0.781 22 :1@C8_:2@C2 79615 0.961 4.99 0.897 23 :1@N3_:2@N6 79464 0.959 4.4 0.864 24 :1@N7_:2@N1 79376 0.958 4.82 0.987 25 :1@N9_:2@C8 79337 0.957 5.6 0.751 26 :1@C4_:2@N1 79200 0.956 4.66 0.829 27 :1@C5_:2@N1 79181 0.955 4.67 0.869 28 :1@C8_:2@C4 79147 0.955 5.41 0.721 29 :1@C6_:2@N6 79104 0.954 4.53 0.995 30 :1@C8_:2@N3 79032 0.954 5.3 0.741 31 :1@N3_:2@C6 78864 0.952 4.46 0.842 32 :1@C4_:2@N9 78820 0.951 5.81 0.584 33 :1@C8_:2@C6 78764 0.95 4.97 1.01 34 :1@C6_:2@C6 78174 0.943 4.89 0.848 35 :1@C2_:2@N7 78111 0.942 5.21 0.866 36 :1@C4_:2@C8 78002 0.941 5.66 0.772 37 :1@C8_:2@C5 77371 0.933 5.24 0.918 38 :1@N7_:2@C2 77324 0.933 5.1 0.896 39 :1@N1_:2@N6 77279 0.932 4.36 0.936 40 :1@N3_:2@C4 76928 0.928 5.25 0.667 41 :1@C2_:2@N6 76903 0.928 4.19 0.955 42 :1@C5_:2@C4 76875 0.928 5.66 0.657 43 :1@N7_:2@C6 76776 0.926 4.93 0.986 44 :1@C2_:2@C5 76246 0.92 5.01 0.735 45 :1@C4_:2@N3 75777 0.914 5.34 0.697 46 :1@C4_:2@C2 75693 0.913 5 0.825 47 :1@C2_:2@C6 75241 0.908 4.53 0.88 48 :1@N3_:2@N9 75007 0.905 5.75 0.591 49 :1@C5_:2@C2 74786 0.902 5.07 0.833 50 :1@N1_:2@C6 74732 0.902 4.8 0.798 51 :1@C6_:2@C5 74440 0.898 5.54 0.791 52 :1@C6_:2@N1 74112 0.894 4.83 0.855 53 :1@N7_:2@N3 73999 0.893 5.6 0.74 54 :1@N3_:2@N1 73388 0.885 4.75 0.96 55 :1@N1_:2@C5 73162 0.883 5.46 0.724 56 :1@N6_:2@N6 72984 0.881 4.89 1.06 57 :1@N7_:2@C4 72673 0.877 5.73 0.699 58 :1@N7_:2@N6 71611 0.864 4.81 1.13 59 :1@C8_:2@N6 71596 0.864 5.06 1.11 60 :1@C5_:2@N3 71402 0.861 5.58 0.677 61 :1@N7_:2@C5 71159 0.859 5.35 0.864 62 :1@N6_:2@C6 70631 0.852 5.38 0.871 63 :1@N1_:2@N1 70053 0.845 4.89 0.924 64 :1@C2_:2@N1 69889 0.843 4.8 1.06 65 :1@N6_:2@N1 69788 0.842 5.25 0.842 66 :1@C5_:2@N7 69186 0.835 5.49 0.92 67 :1@N3_:2@N3 69141 0.834 5.52 0.76 68 :1@C8_:2@N9 69131 0.834 5.95 0.66 69 :1@N3_:2@C2 69104 0.834 5.21 0.926 70 :1@C2_:2@C4 67998 0.82 5.65 0.606 71 :1@C6_:2@C2 67007 0.808 5.37 0.805 72 :1@C8_:2@N7 62863 0.758 5.52 1.01 73 :1@C6_:2@C4 62603 0.755 6.03 0.599 74 :1@C6_:2@N7 61473 0.742 5.71 0.897 75 :1@C2_:2@C2 60440 0.729 5.34 0.941 76 :1@N1_:2@C4 60296 0.727 6.05 0.527 77 :1@N1_:2@C2 59586 0.719 5.47 0.838 78 :1@C5_:2@N9 58834 0.71 6.23 0.623 79 :1@N6_:2@C2 58287 0.703 5.74 0.723 80 :1@C6_:2@N3 57879 0.698 5.95 0.588 81 :1@C2_:2@N3 56661 0.684 5.81 0.688 82 :1@C8_:2@C8 55405 0.668 5.86 0.853 83 :1@N7_:2@N7 54047 0.652 5.57 0.964 84 :1@C5_:2@C8 54009 0.652 5.97 0.798 85 :1@N6_:2@C5 53739 0.648 5.96 0.758 86 :1@N1_:2@N3 50999 0.615 6.05 0.576 87 :1@N7_:2@N9 48683 0.587 6.2 0.641 88 :1@N7_:2@C8 39695 0.479 5.95 0.81 89 :1@N6_:2@N3 38387 0.463 6.3 0.549 90 :1@N6_:2@C4 32411 0.391 6.33 0.613 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0042 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 82883 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 82883 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 82883 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 82883 COM "COM" (double, distance), size is 82883 v_base1 "v_base1" (vector), size is 82883 v_base2 "v_base2" (vector), size is 82883 normalangle "normalangle" (double), size is 82883 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: 0.6719 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.