CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/08/15 12:15:49 | Available memory: 1603.39 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.c0] Reading '../ctraj.c0' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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_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,N2,H21,H22,N7,C8,H8,N9,O6 :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,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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: 0: [traj] 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 203546 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 203546 of 203546) Coordinate processing will occur on 203546 frames. TIME: Run Initialization took 0.0001 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 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.c0 (1-203546, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 118 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@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@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@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@O6' to ':2@N9' Atom ':1@O6' to ':2@C8' Atom ':1@O6' to ':2@N7' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@N2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' 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@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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 203546 frames and processed 203546 frames. TIME: Trajectory processing: 2.6714 s TIME: Avg. throughput= 76193.5065 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 112.313 118 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 203376 0.999 4.22 0.399 2 :1@C4_:2@N7 203331 0.999 4.33 0.629 3 :1@C4_:2@C4 203312 0.999 4.43 0.47 4 :1@N9_:2@N9 203303 0.999 4.92 0.523 5 :1@C4_:2@N9 203279 0.999 4.65 0.799 6 :1@C5_:2@C5 203270 0.999 4.15 0.582 7 :1@N9_:2@C5 203251 0.999 4.66 0.53 8 :1@N3_:2@C4 203172 0.998 4.39 0.523 9 :1@C6_:2@C5 203131 0.998 4.29 0.803 10 :1@C6_:2@C6 203083 0.998 3.97 0.49 11 :1@N3_:2@C5 203016 0.997 4.43 0.504 12 :1@C4_:2@C6 202999 0.997 4.49 0.702 13 :1@N9_:2@C4 202987 0.997 4.89 0.509 14 :1@C5_:2@C6 202985 0.997 4.1 0.52 15 :1@C4_:2@C8 202854 0.997 4.53 0.901 16 :1@N9_:2@N7 202827 0.996 4.51 0.64 17 :1@C6_:2@O6 202815 0.996 4.03 0.649 18 :1@C5_:2@C4 202804 0.996 4.62 0.742 19 :1@O6_:2@C6 202744 0.996 4.16 0.738 20 :1@C5_:2@O6 202649 0.996 4.24 0.701 21 :1@C6_:2@N1 202601 0.995 4.18 0.583 22 :1@N1_:2@C6 202598 0.995 4.23 0.574 23 :1@N3_:2@N9 202592 0.995 4.54 0.91 24 :1@N3_:2@N3 202519 0.995 4.73 0.563 25 :1@O6_:2@O6 202510 0.995 4 0.638 26 :1@C4_:2@N3 202473 0.995 4.91 0.553 27 :1@N1_:2@N1 202459 0.995 4.27 0.626 28 :1@N1_:2@C5 202402 0.994 4.43 0.77 29 :1@C5_:2@N7 202398 0.994 4.36 0.834 30 :1@N3_:2@N7 202254 0.994 4.64 0.661 31 :1@C8_:2@C5 202243 0.994 4.81 0.652 32 :1@C2_:2@C4 202233 0.994 4.46 0.83 33 :1@N7_:2@C5 202233 0.994 4.56 0.707 34 :1@C4_:2@O6 202200 0.993 4.87 0.895 35 :1@C5_:2@N1 202198 0.993 4.51 0.71 36 :1@N9_:2@C8 202190 0.993 4.63 0.753 37 :1@C2_:2@C5 202076 0.993 4.49 0.623 38 :1@N3_:2@C6 202050 0.993 4.77 0.844 39 :1@O6_:2@N1 201982 0.992 4.3 0.872 40 :1@N1_:2@C2 201800 0.991 4.51 0.845 41 :1@N7_:2@C6 201781 0.991 4.51 0.718 42 :1@C2_:2@C2 201537 0.99 4.67 0.723 43 :1@C2_:2@N1 201520 0.99 4.65 0.83 44 :1@C4_:2@N1 201507 0.99 4.86 0.901 45 :1@C2_:2@C6 201420 0.99 4.59 0.743 46 :1@C6_:2@C2 201405 0.989 4.66 0.83 47 :1@N3_:2@C2 201323 0.989 4.97 0.789 48 :1@N3_:2@C8 201283 0.989 4.65 0.926 49 :1@C2_:2@N3 201196 0.988 4.59 0.831 50 :1@N9_:2@C6 201124 0.988 5.08 0.826 51 :1@C8_:2@C4 201062 0.988 5.28 0.634 52 :1@N1_:2@O6 200963 0.987 4.46 0.884 53 :1@C5_:2@N3 200908 0.987 5.06 0.724 54 :1@C4_:2@C2 200869 0.987 5.05 0.765 55 :1@C6_:2@C4 200856 0.987 4.72 1.05 56 :1@N7_:2@C4 200725 0.986 5.18 0.738 57 :1@N3_:2@N1 200667 0.986 4.97 0.993 58 :1@N1_:2@C4 200644 0.986 4.6 1.08 59 :1@C5_:2@C2 200483 0.985 4.94 0.708 60 :1@N7_:2@O6 200203 0.984 4.47 0.753 61 :1@C6_:2@N7 199967 0.982 4.74 0.947 62 :1@O6_:2@C5 199876 0.982 4.74 0.989 63 :1@C8_:2@C6 199268 0.979 5.02 0.782 64 :1@N1_:2@N3 198850 0.977 4.67 1.13 65 :1@C8_:2@N9 198639 0.976 5.42 0.656 66 :1@C5_:2@N9 198521 0.975 5.05 0.979 67 :1@C2_:2@N7 198292 0.974 4.87 0.844 68 :1@C8_:2@N7 197509 0.97 4.56 0.806 69 :1@C6_:2@N3 197298 0.969 4.93 1.04 70 :1@N2_:2@C5 197159 0.969 5.09 0.72 71 :1@C5_:2@C8 197116 0.968 4.83 1 72 :1@N1_:2@N7 196944 0.968 4.93 0.933 73 :1@N2_:2@C4 196793 0.967 4.85 0.875 74 :1@C2_:2@O6 196783 0.967 4.99 1.08 75 :1@N7_:2@N7 196668 0.966 4.51 0.86 76 :1@N7_:2@N1 196412 0.965 5 0.921 77 :1@N9_:2@N3 196334 0.965 5.43 0.787 78 :1@C8_:2@O6 195967 0.963 5.13 0.796 79 :1@N3_:2@O6 195094 0.958 5.23 1.06 80 :1@N2_:2@C6 194880 0.957 5.21 0.876 81 :1@N9_:2@O6 194608 0.956 5.39 0.852 82 :1@C2_:2@N9 194067 0.953 4.74 1.16 83 :1@N2_:2@N1 193991 0.953 5.08 0.98 84 :1@N1_:2@N2 193721 0.952 4.95 0.902 85 :1@C2_:2@N2 193303 0.95 5.15 0.873 86 :1@N2_:2@C2 192748 0.947 4.89 0.892 87 :1@N2_:2@N3 192619 0.946 4.75 0.932 88 :1@C6_:2@N2 192436 0.945 5.22 0.842 89 :1@O6_:2@C2 192425 0.945 4.84 1.12 90 :1@C8_:2@C8 192186 0.944 4.89 0.776 91 :1@C2_:2@C8 189428 0.931 4.93 1.05 92 :1@N7_:2@N9 188719 0.927 5.48 0.803 93 :1@O6_:2@N7 186867 0.918 5.18 0.959 94 :1@N7_:2@C8 186643 0.917 5.02 0.836 95 :1@N7_:2@N3 185722 0.912 5.61 0.779 96 :1@N3_:2@N2 185195 0.91 5.53 0.899 97 :1@N7_:2@C2 184593 0.907 5.44 0.924 98 :1@C5_:2@N2 183478 0.901 5.56 0.781 99 :1@N2_:2@N7 180242 0.886 5.38 0.9 100 :1@C8_:2@N3 178662 0.878 5.72 0.824 101 :1@C6_:2@C8 178433 0.877 5.13 1.03 102 :1@N9_:2@N1 178312 0.876 5.36 1.01 103 :1@C8_:2@N1 177276 0.871 5.39 0.993 104 :1@O6_:2@C4 176481 0.867 5.07 1.1 105 :1@N2_:2@N9 175513 0.862 4.91 1.08 106 :1@C4_:2@N2 174788 0.859 5.62 0.827 107 :1@N1_:2@C8 172504 0.847 5.08 1.04 108 :1@N9_:2@C2 172229 0.846 5.46 0.993 109 :1@N1_:2@N9 172151 0.846 4.89 1.15 110 :1@O6_:2@N2 172026 0.845 5.13 1.06 111 :1@N2_:2@N2 171690 0.843 4.97 0.988 112 :1@C6_:2@N9 169655 0.833 5.07 1.06 113 :1@O6_:2@N3 165161 0.811 5.07 1.13 114 :1@N2_:2@C8 162501 0.798 5.16 0.896 115 :1@C8_:2@C2 158903 0.781 5.59 1.04 116 :1@N2_:2@O6 158186 0.777 5.35 1.11 117 :1@O6_:2@C8 137964 0.678 5.41 0.765 118 :1@O6_:2@N9 128362 0.631 5.29 0.731 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0160 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 203546 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 203546 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 203546 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 203546 COM "COM" (double, distance), size is 203546 v_base1 "v_base1" (vector, vector), size is 203546 v_base2 "v_base2" (vector, vector), size is 203546 normalangle "normalangle" (double), size is 203546 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: 3.2410 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.