CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 14:44:28 | Available memory: 1.599 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.c2] Reading '../ctraj.c2' 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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 93027 of 93027) Coordinate processing will occur on 93027 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.c2 (1-93027, 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 110 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@N2' 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@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@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@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@O6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N2' 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@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@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@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 93027 frames and processed 93027 frames. TIME: Avg. throughput= 80814.8288 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 102.414 110 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 91931 0.988 4.32 0.726 2 :1@C4_:2@N9 91764 0.986 4.45 0.706 3 :1@N3_:2@C4 91635 0.985 4.37 0.579 4 :1@N3_:2@C8 91548 0.984 4.5 0.795 5 :1@C4_:2@C8 91525 0.984 4.4 0.84 6 :1@N9_:2@N9 91213 0.981 4.82 0.582 7 :1@C2_:2@C4 91211 0.98 4.34 0.752 8 :1@N3_:2@C5 91151 0.98 4.58 0.655 9 :1@C2_:2@N9 91149 0.98 4.51 0.923 10 :1@N3_:2@N7 91137 0.98 4.69 0.719 11 :1@C4_:2@C4 91132 0.98 4.34 0.495 12 :1@N3_:2@N3 90956 0.978 4.72 0.617 13 :1@C4_:2@N7 90921 0.977 4.34 0.68 14 :1@C4_:2@C5 90896 0.977 4.27 0.504 15 :1@N9_:2@C8 90684 0.975 4.56 0.805 16 :1@C2_:2@N3 90649 0.974 4.47 0.807 17 :1@N9_:2@C4 90619 0.974 4.87 0.56 18 :1@N1_:2@C4 90587 0.974 4.39 0.872 19 :1@N9_:2@C5 90546 0.973 4.71 0.543 20 :1@C5_:2@C4 90522 0.973 4.38 0.666 21 :1@C4_:2@N3 90513 0.973 4.81 0.571 22 :1@C2_:2@C5 90434 0.972 4.57 0.761 23 :1@N9_:2@N7 90391 0.972 4.54 0.709 24 :1@C5_:2@C5 90372 0.971 4.05 0.61 25 :1@C6_:2@C4 90296 0.971 4.39 0.827 26 :1@C4_:2@C6 90142 0.969 4.71 0.669 27 :1@C6_:2@C5 90128 0.969 4.14 0.712 28 :1@C5_:2@N3 90075 0.968 4.79 0.651 29 :1@N1_:2@C5 90039 0.968 4.42 0.768 30 :1@C5_:2@C6 90015 0.968 4.14 0.576 31 :1@C6_:2@C6 89887 0.966 4.03 0.606 32 :1@C6_:2@N3 89863 0.966 4.57 0.831 33 :1@N1_:2@N3 89845 0.966 4.4 0.946 34 :1@C6_:2@C2 89758 0.965 4.41 0.704 35 :1@C6_:2@N1 89725 0.965 4.16 0.622 36 :1@C5_:2@N1 89689 0.964 4.49 0.712 37 :1@C5_:2@C2 89656 0.964 4.77 0.697 38 :1@C2_:2@C8 89656 0.964 4.81 0.91 39 :1@C5_:2@O6 89610 0.963 4.44 0.682 40 :1@C2_:2@C2 89585 0.963 4.77 0.843 41 :1@C5_:2@N7 89525 0.962 4.27 0.819 42 :1@N1_:2@C2 89521 0.962 4.41 0.875 43 :1@N1_:2@N1 89507 0.962 4.44 0.83 44 :1@C8_:2@C5 89490 0.962 4.71 0.734 45 :1@C8_:2@C4 89471 0.962 5.14 0.729 46 :1@N6_:2@C6 89469 0.962 4.07 0.712 47 :1@N1_:2@C6 89434 0.961 4.46 0.794 48 :1@C4_:2@C2 89419 0.961 5.09 0.769 49 :1@N7_:2@C6 89403 0.961 4.35 0.777 50 :1@C6_:2@O6 89371 0.961 4.33 0.79 51 :1@N7_:2@C5 89228 0.959 4.36 0.776 52 :1@N6_:2@N1 89218 0.959 4.08 0.731 53 :1@N6_:2@O6 89204 0.959 4.14 0.821 54 :1@C4_:2@N1 89187 0.959 5.04 0.838 55 :1@N9_:2@C6 89167 0.959 5.22 0.72 56 :1@N3_:2@C2 89128 0.958 5.15 0.773 57 :1@N7_:2@C4 89047 0.957 4.91 0.779 58 :1@C2_:2@N7 89002 0.957 4.87 0.863 59 :1@C5_:2@N9 88993 0.957 4.74 0.836 60 :1@N6_:2@C2 88881 0.955 4.52 0.958 61 :1@C8_:2@C6 88814 0.955 4.97 0.816 62 :1@C6_:2@N7 88803 0.955 4.6 0.887 63 :1@N7_:2@O6 88797 0.955 4.43 0.764 64 :1@N3_:2@C6 88702 0.954 5.1 0.813 65 :1@N6_:2@C5 88691 0.953 4.52 0.837 66 :1@C4_:2@O6 88561 0.952 5.18 0.741 67 :1@N7_:2@N1 88318 0.949 4.82 0.963 68 :1@N1_:2@N7 88154 0.948 4.9 0.905 69 :1@C2_:2@C6 88031 0.946 4.89 0.853 70 :1@C6_:2@N2 88022 0.946 4.99 0.815 71 :1@C2_:2@N1 88004 0.946 4.96 0.876 72 :1@N9_:2@N3 87926 0.945 5.41 0.826 73 :1@C8_:2@O6 87700 0.943 5.15 0.785 74 :1@C5_:2@C8 87623 0.942 4.6 0.883 75 :1@C8_:2@N9 87540 0.941 5.25 0.698 76 :1@N1_:2@N9 87345 0.939 4.79 0.963 77 :1@N3_:2@N1 87062 0.936 5.31 0.867 78 :1@N7_:2@N3 86946 0.935 5.39 0.839 79 :1@C8_:2@N7 86936 0.935 4.47 0.852 80 :1@N7_:2@N7 86457 0.929 4.35 0.864 81 :1@N1_:2@C8 86046 0.925 5.06 0.945 82 :1@N9_:2@O6 86043 0.925 5.61 0.68 83 :1@N6_:2@N3 85585 0.92 4.89 1.02 84 :1@N6_:2@C4 85559 0.92 4.84 0.895 85 :1@N1_:2@O6 85491 0.919 4.85 0.94 86 :1@C6_:2@N9 85363 0.918 4.86 0.896 87 :1@C6_:2@C8 84985 0.914 4.94 0.907 88 :1@N7_:2@C2 84906 0.913 5.22 0.96 89 :1@C8_:2@C8 84847 0.912 4.75 0.814 90 :1@N7_:2@N9 84647 0.91 5.22 0.77 91 :1@N6_:2@N2 84563 0.909 4.87 1.02 92 :1@C5_:2@N2 84399 0.907 5.43 0.805 93 :1@N6_:2@N7 84244 0.906 5.04 0.896 94 :1@N1_:2@N2 84147 0.905 4.76 0.898 95 :1@C2_:2@N2 83965 0.903 5.23 0.915 96 :1@N7_:2@C8 82859 0.891 4.81 0.805 97 :1@N3_:2@O6 80479 0.865 5.61 0.884 98 :1@C8_:2@N3 80145 0.862 5.57 0.883 99 :1@N3_:2@N2 79909 0.859 5.71 0.813 100 :1@C2_:2@O6 79883 0.859 5.35 0.984 101 :1@C8_:2@N1 79245 0.852 5.3 1.02 102 :1@N9_:2@N1 78860 0.848 5.5 0.94 103 :1@C4_:2@N2 77082 0.829 5.65 0.824 104 :1@N9_:2@C2 75905 0.816 5.51 0.987 105 :1@N6_:2@C8 74127 0.797 5.44 0.776 106 :1@N6_:2@N9 73542 0.791 5.35 0.744 107 :1@C8_:2@C2 70291 0.756 5.41 1.05 108 :1@N7_:2@N2 62897 0.676 5.47 0.984 109 :1@N9_:2@N2 47023 0.505 5.52 1.04 110 :1@C8_:2@N2 44665 0.48 5.34 1.17 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 93027, 'v_base2' size 93027, output size 93027 TIME: Analyses took 0.0082 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 93027 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 93027 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 93027 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 93027 COM "COM" (double, distance), size is 93027 v_base1 "v_base1" (vector, vector), size is 93027 v_base2 "v_base2" (vector, vector), size is 93027 normalangle "normalangle" (double), size is 93027 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0021 s ( 0.18%) TIME: Trajectory Process : 1.1511 s ( 99.08%) TIME: Action Post : 0.0003 s ( 0.02%) TIME: Analysis : 0.0082 s ( 0.71%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.1618 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: 1.4153 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.