CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:13:49 | Available memory: 1.231 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.c1] Reading '../ctraj.c1' 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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] [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 31448 of 31448) Coordinate processing will occur on 31448 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c1 (1-31448, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 110 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@N7' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@O6' Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@N2' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C4' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@O6' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@N2' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@O6' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N2' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@O6' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N2' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@O6' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@N2' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@O6' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@N2' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@O6' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@N2' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@O6' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@N2' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C4' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@O6' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@N2' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 31448 frames and processed 31448 frames. TIME: Avg. throughput= 53684.7676 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 103.893 110 # Contact Nframes Frac. Avg Stdev 1 :2@N9_:1@C4 31394 0.998 4.78 0.787 2 :2@C4_:1@N3 31373 0.998 4.43 0.528 3 :2@C4_:1@C4 31331 0.996 4.52 0.473 4 :2@C5_:1@N3 31318 0.996 4.49 0.514 5 :2@N9_:1@N3 31303 0.995 4.65 0.925 6 :2@C5_:1@C4 31273 0.994 4.26 0.432 7 :2@N9_:1@N9 31246 0.994 4.98 0.5 8 :2@C4_:1@C2 31239 0.993 4.51 0.838 9 :2@N3_:1@N3 31220 0.993 4.67 0.596 10 :2@C5_:1@C2 31209 0.992 4.59 0.679 11 :2@N7_:1@N3 31203 0.992 4.78 0.756 12 :2@C4_:1@N9 31193 0.992 4.95 0.526 13 :2@C8_:1@C4 31191 0.992 4.64 0.94 14 :2@N3_:1@C4 31175 0.991 4.97 0.589 15 :2@N7_:1@C4 31150 0.991 4.38 0.691 16 :2@C6_:1@C4 31132 0.99 4.48 0.685 17 :2@C5_:1@N9 31129 0.99 4.64 0.524 18 :2@C6_:1@N3 31129 0.99 4.73 0.776 19 :2@C8_:1@N9 31088 0.989 4.63 0.703 20 :2@C4_:1@C5 31072 0.988 4.75 0.686 21 :2@N7_:1@N9 31071 0.988 4.46 0.578 22 :2@N1_:1@N1 31069 0.988 4.16 0.684 23 :2@C6_:1@N1 31061 0.988 4.23 0.614 24 :2@C5_:1@N1 31057 0.988 4.55 0.834 25 :2@C6_:1@C2 31050 0.987 4.56 0.701 26 :2@C6_:1@C5 31043 0.987 4.14 0.518 27 :2@C5_:1@C5 31031 0.987 4.22 0.543 28 :2@N1_:1@C6 31016 0.986 4.18 0.634 29 :2@C6_:1@C6 31004 0.986 4.01 0.51 30 :2@N1_:1@C2 30995 0.986 4.5 0.871 31 :2@C5_:1@C6 30980 0.985 4.4 0.794 32 :2@C2_:1@N3 30977 0.985 4.83 0.884 33 :2@N3_:1@C2 30970 0.985 4.5 0.763 34 :2@C2_:1@C2 30969 0.985 4.47 0.759 35 :2@N1_:1@C5 30967 0.985 4.57 0.771 36 :2@C2_:1@N1 30951 0.984 4.38 0.769 37 :2@N7_:1@C5 30951 0.984 4.43 0.846 38 :2@N6_:1@C5 30950 0.984 4.21 0.671 39 :2@N6_:1@C4 30937 0.984 4.84 0.843 40 :2@N1_:1@C4 30928 0.983 4.87 0.95 41 :2@C5_:1@N7 30915 0.983 4.61 0.628 42 :2@C5_:1@C8 30912 0.983 4.8 0.618 43 :2@C6_:1@N9 30905 0.983 5.07 0.834 44 :2@N6_:1@C6 30901 0.983 4.01 0.625 45 :2@C6_:1@O6 30900 0.983 4.24 0.719 46 :2@C2_:1@C4 30878 0.982 5.05 0.845 47 :2@C8_:1@N3 30876 0.982 4.79 1 48 :2@N6_:1@O6 30866 0.981 3.99 0.636 49 :2@C6_:1@N7 30849 0.981 4.57 0.686 50 :2@N6_:1@N7 30843 0.981 4.44 0.754 51 :2@C2_:1@C6 30837 0.981 4.68 0.78 52 :2@N1_:1@N3 30811 0.98 4.88 1.01 53 :2@C4_:1@N1 30803 0.979 4.7 1.05 54 :2@N3_:1@C5 30792 0.979 5.18 0.694 55 :2@N1_:1@O6 30771 0.978 4.33 0.785 56 :2@C2_:1@C5 30737 0.977 5.01 0.752 57 :2@C4_:1@C8 30728 0.977 5.37 0.62 58 :2@C4_:1@C6 30706 0.976 4.86 0.984 59 :2@N6_:1@N1 30675 0.975 4.47 0.823 60 :2@C4_:1@N7 30631 0.974 5.32 0.666 61 :2@N9_:1@C8 30628 0.974 5.51 0.59 62 :2@C6_:1@C8 30583 0.972 5.05 0.803 63 :2@C5_:1@O6 30574 0.972 4.89 0.964 64 :2@N9_:1@C5 30491 0.97 5.21 0.924 65 :2@N7_:1@C8 30458 0.969 4.5 0.67 66 :2@N7_:1@C6 30458 0.969 4.89 0.991 67 :2@N6_:1@C8 30440 0.968 5.11 0.848 68 :2@N3_:1@N1 30410 0.967 4.64 0.987 69 :2@C4_:1@N2 30362 0.965 4.85 0.905 70 :2@C5_:1@N2 30353 0.965 5.17 0.749 71 :2@N7_:1@N7 30334 0.965 4.52 0.772 72 :2@C8_:1@C5 30205 0.96 4.96 1 73 :2@N7_:1@C2 30186 0.96 5.07 0.893 74 :2@C2_:1@N2 30177 0.96 4.61 0.869 75 :2@N3_:1@C6 30092 0.957 5.02 0.923 76 :2@C6_:1@N2 30064 0.956 5.15 0.782 77 :2@N3_:1@N2 30056 0.956 4.57 0.858 78 :2@C8_:1@C8 30049 0.956 4.92 0.689 79 :2@N6_:1@N9 30046 0.955 5.36 0.854 80 :2@N3_:1@N9 29979 0.953 5.53 0.771 81 :2@N6_:1@C2 29977 0.953 4.99 0.937 82 :2@N1_:1@N2 29966 0.953 4.87 0.944 83 :2@N6_:1@N3 29895 0.951 5.23 0.937 84 :2@N1_:1@N7 29836 0.949 5.14 0.883 85 :2@N9_:1@C2 29751 0.946 4.88 1.17 86 :2@N7_:1@N1 29486 0.938 5.12 0.969 87 :2@C2_:1@O6 29464 0.937 4.92 0.963 88 :2@C8_:1@N7 29300 0.932 5.13 0.801 89 :2@N9_:1@N7 29249 0.93 5.65 0.723 90 :2@C8_:1@C2 28061 0.892 5.09 1.08 91 :2@N3_:1@N7 27994 0.89 5.8 0.725 92 :2@N7_:1@O6 27770 0.883 5.32 0.97 93 :2@C2_:1@N7 27597 0.878 5.6 0.857 94 :2@C4_:1@O6 27262 0.867 5.29 1.03 95 :2@N9_:1@N2 26758 0.851 5.01 1.13 96 :2@N1_:1@N9 26666 0.848 5.39 0.978 97 :2@N3_:1@O6 26323 0.837 5.33 1.03 98 :2@C8_:1@C6 26269 0.835 5.27 1.04 99 :2@N9_:1@N1 26164 0.832 5.08 1.17 100 :2@N1_:1@C8 26145 0.831 5.48 0.92 101 :2@N3_:1@C8 26057 0.829 5.86 0.751 102 :2@N6_:1@N2 25958 0.825 5.51 0.949 103 :2@N9_:1@C6 25793 0.82 5.28 1.05 104 :2@N7_:1@N2 25793 0.82 5.53 0.813 105 :2@C2_:1@N9 25593 0.814 5.51 0.934 106 :2@C8_:1@N1 24811 0.789 5.23 1.06 107 :2@C8_:1@N2 23162 0.737 5.3 0.891 108 :2@C2_:1@C8 22730 0.723 5.7 0.898 109 :2@C8_:1@O6 19027 0.605 5.51 0.768 110 :2@N9_:1@O6 17739 0.564 5.44 0.725 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 31448, 'v_base2' size 31448, output size 31448 TIME: Analyses took 0.0042 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 31448 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 31448 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 31448 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 31448 COM "COM" (double, distance), size is 31448 v_base1 "v_base1" (vector, vector), size is 31448 v_base2 "v_base2" (vector, vector), size is 31448 normalangle "normalangle" (double), size is 31448 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.5858 s ( 99.23%) TIME: Action Post : 0.0003 s ( 0.05%) TIME: Analysis : 0.0042 s ( 0.71%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5904 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: 0.7305 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.