CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:35:29 | Available memory: 8367.9 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, 27455 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 27455 of 27455) Coordinate processing will occur on 27455 frames. TIME: Run Initialization took 0.0000 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] 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 (1-27455, 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 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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 27455 frames and processed 27455 frames. TIME: Trajectory processing: 2.3396 s TIME: Avg. throughput= 11734.7966 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 83.4219 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 27420 0.999 4.4 0.466 2 :1@C4_:2@N9 27411 0.998 4.33 0.57 3 :1@N9_:2@N9 27407 0.998 4.77 0.482 4 :1@C4_:2@C5 27404 0.998 4.31 0.484 5 :1@N9_:2@C8 27373 0.997 4.33 0.568 6 :1@C4_:2@C8 27343 0.996 4.18 0.696 7 :1@C5_:2@C4 27343 0.996 4.38 0.601 8 :1@C4_:2@N7 27342 0.996 4.2 0.619 9 :1@N9_:2@N7 27303 0.994 4.35 0.543 10 :1@N3_:2@C4 27298 0.994 4.38 0.536 11 :1@N9_:2@C4 27297 0.994 5.02 0.558 12 :1@N3_:2@N9 27278 0.994 4.22 0.668 13 :1@C5_:2@N9 27278 0.994 4.64 0.712 14 :1@C6_:2@C4 27268 0.993 4.27 0.712 15 :1@N9_:2@C5 27268 0.993 4.78 0.544 16 :1@C5_:2@C5 27243 0.992 4.02 0.501 17 :1@N3_:2@C5 27228 0.992 4.63 0.604 18 :1@C4_:2@N3 27226 0.992 5.01 0.6 19 :1@N3_:2@C8 27185 0.99 4.38 0.808 20 :1@C4_:2@C6 27183 0.99 4.88 0.634 21 :1@N1_:2@C4 27176 0.99 4.21 0.762 22 :1@N3_:2@N7 27173 0.99 4.67 0.73 23 :1@C5_:2@N3 27173 0.99 4.92 0.709 24 :1@C6_:2@C5 27171 0.99 4.05 0.637 25 :1@C2_:2@C4 27164 0.989 4.23 0.686 26 :1@C6_:2@N3 27145 0.989 4.49 0.753 27 :1@C5_:2@C6 27143 0.989 4.27 0.552 28 :1@C5_:2@N7 27140 0.989 4.09 0.671 29 :1@N1_:2@C5 27123 0.988 4.35 0.784 30 :1@C5_:2@C8 27099 0.987 4.43 0.745 31 :1@C6_:2@C6 27096 0.987 4.03 0.569 32 :1@C6_:2@C2 27094 0.987 4.42 0.667 33 :1@C6_:2@N1 27076 0.986 4.24 0.593 34 :1@N7_:2@C5 27057 0.986 4.35 0.652 35 :1@C2_:2@C5 27049 0.985 4.56 0.75 36 :1@C2_:2@N9 27047 0.985 4.35 0.868 37 :1@C8_:2@N9 27046 0.985 5.23 0.629 38 :1@C8_:2@C8 27042 0.985 4.62 0.633 39 :1@C5_:2@N1 27036 0.985 4.79 0.698 40 :1@C8_:2@C5 27002 0.984 4.75 0.681 41 :1@N7_:2@C4 27000 0.983 4.99 0.742 42 :1@C5_:2@C2 27000 0.983 5.02 0.737 43 :1@N7_:2@N7 26993 0.983 4.19 0.665 44 :1@N6_:2@N1 26983 0.983 4.05 0.657 45 :1@N1_:2@C6 26981 0.983 4.42 0.783 46 :1@C8_:2@N7 26980 0.983 4.29 0.632 47 :1@C5_:2@N6 26966 0.982 4.56 0.677 48 :1@N6_:2@C6 26963 0.982 3.99 0.633 49 :1@C8_:2@C4 26959 0.982 5.29 0.716 50 :1@N1_:2@N1 26955 0.982 4.4 0.757 51 :1@N6_:2@C5 26952 0.982 4.4 0.738 52 :1@C6_:2@N7 26951 0.982 4.49 0.822 53 :1@N7_:2@C6 26936 0.981 4.55 0.757 54 :1@N7_:2@C8 26896 0.98 4.73 0.69 55 :1@C6_:2@N6 26889 0.979 4.38 0.762 56 :1@N6_:2@C2 26880 0.979 4.42 0.862 57 :1@N7_:2@N9 26846 0.978 5.21 0.707 58 :1@N6_:2@N6 26827 0.977 4.1 0.789 59 :1@N6_:2@C4 26794 0.976 4.75 0.841 60 :1@N9_:2@C6 26780 0.975 5.46 0.719 61 :1@C6_:2@N9 26774 0.975 4.77 0.829 62 :1@C4_:2@N1 26767 0.975 5.39 0.772 63 :1@N3_:2@C6 26690 0.972 5.24 0.72 64 :1@N7_:2@N6 26640 0.97 4.54 0.747 65 :1@C2_:2@N7 26607 0.969 4.89 0.878 66 :1@C4_:2@N6 26592 0.969 5.36 0.703 67 :1@C2_:2@C6 26578 0.968 4.93 0.798 68 :1@C8_:2@C6 26564 0.968 5.21 0.823 69 :1@N1_:2@N9 26492 0.965 4.62 0.882 70 :1@N1_:2@N7 26475 0.964 4.87 0.906 71 :1@C2_:2@C8 26428 0.963 4.71 0.909 72 :1@C6_:2@C8 26418 0.962 4.82 0.829 73 :1@N7_:2@N1 26410 0.962 5.24 0.914 74 :1@N6_:2@N7 26312 0.958 4.98 0.828 75 :1@C8_:2@N6 26024 0.948 5.29 0.801 76 :1@N1_:2@N6 25889 0.943 4.94 0.891 77 :1@N1_:2@C8 25646 0.934 4.92 0.871 78 :1@N7_:2@N3 25519 0.929 5.62 0.862 79 :1@N9_:2@N6 25235 0.919 5.77 0.699 80 :1@N7_:2@C2 24637 0.897 5.6 0.913 81 :1@N6_:2@C8 24075 0.877 5.42 0.704 82 :1@N3_:2@N6 23821 0.868 5.81 0.717 83 :1@N6_:2@N9 23756 0.865 5.29 0.675 84 :1@C2_:2@N6 23738 0.865 5.5 0.813 85 :1@C8_:2@N3 22023 0.802 5.89 0.785 86 :1@C8_:2@N1 21557 0.785 5.75 0.878 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0025 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 27455 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 27455 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 27455 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 27455 COM "COM" (double, distance), size is 27455 v_base1 "v_base1" (vector), size is 27455 v_base2 "v_base2" (vector), size is 27455 normalangle "normalangle" (double), size is 27455 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: 2.4271 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.