CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/17/16 14:16:52 | Available memory: 2518.93 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.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] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 67414 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 67414 of 67414) Coordinate processing will occur on 67414 frames. TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 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] 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] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c2 (1-67414, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 86 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@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@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@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@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@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@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@N3' Atom ':1@C4' to ':2@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 67414 frames and processed 67414 frames. TIME: Trajectory processing: 22.7727 s TIME: Avg. throughput= 2960.2932 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 84.2261 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 67384 1 4.22 0.457 2 :1@C4_:2@C4 67369 0.999 4.37 0.415 3 :1@C4_:2@C5 67360 0.999 4.27 0.419 4 :1@N9_:2@N9 67359 0.999 4.74 0.423 5 :1@C4_:2@N7 67329 0.999 4.07 0.533 6 :1@C4_:2@C8 67324 0.999 4.01 0.579 7 :1@N9_:2@C8 67321 0.999 4.23 0.484 8 :1@C5_:2@C4 67311 0.998 4.33 0.511 9 :1@N9_:2@N7 67290 0.998 4.3 0.489 10 :1@C5_:2@C5 67282 0.998 3.95 0.427 11 :1@N3_:2@C4 67274 0.998 4.3 0.493 12 :1@N3_:2@N9 67263 0.998 4.05 0.573 13 :1@C6_:2@C4 67261 0.998 4.13 0.567 14 :1@C5_:2@N9 67261 0.998 4.53 0.573 15 :1@C6_:2@C5 67218 0.997 3.9 0.538 16 :1@N9_:2@C5 67216 0.997 4.83 0.513 17 :1@N9_:2@C4 67213 0.997 5.08 0.535 18 :1@C5_:2@N7 67207 0.997 3.94 0.582 19 :1@N3_:2@C5 67180 0.997 4.56 0.557 20 :1@N1_:2@C4 67136 0.996 4.01 0.646 21 :1@N3_:2@C8 67133 0.996 4.18 0.706 22 :1@C5_:2@C8 67129 0.996 4.27 0.623 23 :1@C5_:2@C6 67115 0.996 4.28 0.51 24 :1@C6_:2@C6 67113 0.996 3.95 0.51 25 :1@C2_:2@C4 67113 0.996 4.06 0.626 26 :1@C4_:2@C6 67104 0.995 4.93 0.563 27 :1@N3_:2@N7 67091 0.995 4.52 0.663 28 :1@C4_:2@N3 67073 0.995 5.05 0.574 29 :1@C6_:2@N3 67065 0.995 4.43 0.652 30 :1@N1_:2@C5 67048 0.995 4.16 0.711 31 :1@C6_:2@N1 67009 0.994 4.23 0.546 32 :1@C5_:2@N3 67008 0.994 4.95 0.666 33 :1@N7_:2@C5 67006 0.994 4.37 0.616 34 :1@C2_:2@N9 67002 0.994 4.13 0.743 35 :1@N6_:2@C5 66987 0.994 4.23 0.631 36 :1@N7_:2@N7 66983 0.994 4.12 0.595 37 :1@N6_:2@C6 66966 0.993 3.87 0.564 38 :1@C6_:2@N7 66966 0.993 4.29 0.734 39 :1@C6_:2@C2 66958 0.993 4.41 0.62 40 :1@C8_:2@C8 66958 0.993 4.58 0.566 41 :1@C8_:2@N9 66924 0.993 5.26 0.574 42 :1@C2_:2@C5 66916 0.993 4.42 0.703 43 :1@N6_:2@N1 66904 0.992 3.99 0.599 44 :1@C8_:2@N7 66904 0.992 4.29 0.592 45 :1@C5_:2@N6 66898 0.992 4.59 0.601 46 :1@C8_:2@C5 66877 0.992 4.83 0.664 47 :1@C5_:2@N1 66863 0.992 4.87 0.667 48 :1@N6_:2@C4 66856 0.992 4.62 0.696 49 :1@N1_:2@C6 66854 0.992 4.31 0.731 50 :1@N7_:2@C4 66850 0.992 5.03 0.694 51 :1@C6_:2@N9 66846 0.992 4.62 0.681 52 :1@N7_:2@C8 66831 0.991 4.65 0.598 53 :1@C6_:2@N6 66811 0.991 4.34 0.687 54 :1@N1_:2@N1 66798 0.991 4.36 0.7 55 :1@N6_:2@N6 66780 0.991 4 0.736 56 :1@N7_:2@C6 66772 0.99 4.63 0.748 57 :1@N7_:2@N9 66715 0.99 5.21 0.619 58 :1@C5_:2@C2 66708 0.99 5.11 0.719 59 :1@N6_:2@C2 66686 0.989 4.38 0.776 60 :1@C8_:2@C4 66680 0.989 5.39 0.692 61 :1@N1_:2@N9 66482 0.986 4.43 0.747 62 :1@C6_:2@C8 66417 0.985 4.65 0.722 63 :1@N7_:2@N6 66293 0.983 4.63 0.729 64 :1@C2_:2@N7 66281 0.983 4.72 0.804 65 :1@N9_:2@C6 66271 0.983 5.58 0.669 66 :1@N1_:2@N7 66248 0.983 4.67 0.831 67 :1@C2_:2@C8 66218 0.982 4.5 0.809 68 :1@N3_:2@C6 66217 0.982 5.27 0.629 69 :1@C4_:2@N1 66200 0.982 5.5 0.688 70 :1@N6_:2@N7 66196 0.982 4.8 0.757 71 :1@C4_:2@N6 66128 0.981 5.43 0.61 72 :1@C2_:2@C6 66108 0.981 4.9 0.734 73 :1@C8_:2@C6 65854 0.977 5.35 0.807 74 :1@N1_:2@C8 65321 0.969 4.74 0.78 75 :1@N7_:2@N1 65161 0.967 5.38 0.903 76 :1@N1_:2@N6 64993 0.964 4.91 0.824 77 :1@C8_:2@N6 64665 0.959 5.43 0.781 78 :1@N6_:2@C8 63500 0.942 5.34 0.659 79 :1@N6_:2@N9 63262 0.938 5.27 0.623 80 :1@N7_:2@N3 62804 0.932 5.72 0.828 81 :1@N9_:2@N6 62587 0.928 5.9 0.638 82 :1@C2_:2@N6 60588 0.899 5.56 0.725 83 :1@N3_:2@N6 60353 0.895 5.9 0.609 84 :1@N7_:2@C2 59495 0.883 5.72 0.894 85 :1@C8_:2@N3 51463 0.763 6.01 0.77 86 :1@C8_:2@N1 50055 0.743 5.89 0.864 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0096 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 67414 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 67414 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 67414 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 67414 COM "COM" (double, distance), size is 67414 v_base1 "v_base1" (vector, vector), size is 67414 v_base2 "v_base2" (vector, vector), size is 67414 normalangle "normalangle" (double), size is 67414 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: 23.1119 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.