CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/09/15 15:41:52 | Available memory: 86551.7 MB INPUT: Reading Input from file pt-criteria.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. TIME: Run Initialization took 0.0002 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,K+,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. ----- traj.1.01 (1-50000, 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 98 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@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@N6' 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@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@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@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@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' 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@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' 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@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' 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@N6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 34.2859 s TIME: Avg. throughput= 1458.3257 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 64.7563 98 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 38467 0.769 4.82 0.798 2 :1@N9_:2@N7 38174 0.763 4.87 0.915 3 :1@C4_:2@C5 38125 0.762 4.75 0.837 4 :1@N9_:2@C4 38125 0.762 5.1 0.727 5 :1@N9_:2@N9 37853 0.757 5.37 0.744 6 :1@N9_:2@C8 37786 0.756 5.17 0.899 7 :1@N3_:2@C5 37750 0.755 4.91 0.853 8 :1@C4_:2@C6 37541 0.751 4.75 0.81 9 :1@C4_:2@C4 37473 0.749 4.96 0.846 10 :1@N9_:2@C6 37381 0.748 4.9 0.844 11 :1@N3_:2@C4 37238 0.745 4.95 0.906 12 :1@C4_:2@N7 37214 0.744 4.92 0.943 13 :1@N3_:2@C6 36999 0.74 5.02 0.878 14 :1@N3_:2@N7 36729 0.735 5.06 0.936 15 :1@C4_:2@N6 36535 0.731 4.96 0.87 16 :1@C4_:2@N1 36497 0.73 4.94 0.861 17 :1@C5_:2@C6 36359 0.727 4.61 0.912 18 :1@C8_:2@C5 36185 0.724 4.91 0.906 19 :1@C5_:2@C5 35959 0.719 4.82 0.956 20 :1@C4_:2@C8 35959 0.719 5.18 0.967 21 :1@C4_:2@N9 35945 0.719 5.25 0.891 22 :1@N9_:2@N6 35897 0.718 5.06 0.88 23 :1@N9_:2@N3 35875 0.718 5.37 0.804 24 :1@C4_:2@N3 35852 0.717 5.14 0.875 25 :1@C4_:2@C2 35797 0.716 5.08 0.904 26 :1@N3_:2@N9 35727 0.715 5.11 0.983 27 :1@C8_:2@C6 35724 0.714 4.79 0.952 28 :1@N3_:2@C8 35716 0.714 5.16 0.994 29 :1@C5_:2@N6 35691 0.714 4.66 0.927 30 :1@C5_:2@N1 35626 0.713 4.72 0.94 31 :1@N3_:2@N1 35537 0.711 5.15 0.924 32 :1@N3_:2@N3 35511 0.71 5.09 0.938 33 :1@C8_:2@C4 35199 0.704 5.32 0.807 34 :1@N7_:2@C6 35138 0.703 4.66 0.968 35 :1@N3_:2@C2 35112 0.702 5.15 0.937 36 :1@N9_:2@N1 34975 0.7 5.12 0.884 37 :1@C8_:2@N7 34949 0.699 4.97 1.02 38 :1@N3_:2@N6 34782 0.696 5.28 0.985 39 :1@C8_:2@N6 34690 0.694 4.76 1.01 40 :1@N7_:2@N6 34549 0.691 4.54 1.01 41 :1@N7_:2@C5 34504 0.69 4.94 0.949 42 :1@C2_:2@C5 34422 0.688 5.02 0.92 43 :1@C2_:2@C6 34380 0.688 5.02 0.936 44 :1@C6_:2@C6 34378 0.688 4.73 0.969 45 :1@N7_:2@N1 34218 0.684 4.81 1.02 46 :1@C5_:2@C2 34080 0.682 4.94 1 47 :1@C5_:2@C4 34024 0.68 5.07 0.935 48 :1@C6_:2@N6 33986 0.68 4.78 0.992 49 :1@N9_:2@C2 33957 0.679 5.27 0.888 50 :1@C5_:2@N7 33884 0.678 5.08 1 51 :1@C6_:2@N1 33792 0.676 4.67 0.991 52 :1@C2_:2@N1 33611 0.672 5.03 0.976 53 :1@C8_:2@N1 33534 0.671 4.99 0.983 54 :1@N1_:2@C6 33115 0.662 4.92 0.935 55 :1@C2_:2@C4 33050 0.661 4.95 1.01 56 :1@C8_:2@C8 32858 0.657 5.39 0.923 57 :1@C8_:2@N9 32808 0.656 5.66 0.777 58 :1@N1_:2@N1 32718 0.654 4.83 0.968 59 :1@N7_:2@C4 32642 0.653 5.35 0.87 60 :1@C6_:2@C5 32639 0.653 4.99 0.972 61 :1@C2_:2@N7 32464 0.649 5.28 0.96 62 :1@C5_:2@N3 32405 0.648 5.12 0.962 63 :1@C2_:2@C2 32338 0.647 4.95 0.988 64 :1@N7_:2@N7 32335 0.647 5.13 1.04 65 :1@N7_:2@C2 32098 0.642 5.14 1.03 66 :1@C8_:2@N3 32074 0.641 5.49 0.861 67 :1@N1_:2@C5 31976 0.64 5.09 0.949 68 :1@N1_:2@N6 31865 0.637 5.02 1.02 69 :1@C2_:2@N6 31728 0.635 5.17 1.06 70 :1@C8_:2@C2 31566 0.631 5.24 0.959 71 :1@N6_:2@N6 31528 0.631 4.87 1.06 72 :1@C6_:2@C2 31321 0.626 4.76 1.05 73 :1@C2_:2@N3 31227 0.625 4.87 1.03 74 :1@N6_:2@C6 30969 0.619 4.92 1.01 75 :1@N6_:2@N1 30767 0.615 4.72 1.05 76 :1@N1_:2@C2 30600 0.612 4.76 1.03 77 :1@N7_:2@N3 30484 0.61 5.43 0.927 78 :1@C2_:2@C8 30214 0.604 5.34 0.975 79 :1@C5_:2@C8 30158 0.603 5.4 0.917 80 :1@C2_:2@N9 30028 0.601 5.11 1.02 81 :1@C5_:2@N9 29919 0.598 5.43 0.858 82 :1@C6_:2@C4 29839 0.597 5.06 0.973 83 :1@N1_:2@C4 29763 0.595 5.02 1.02 84 :1@C6_:2@N7 29738 0.595 5.34 0.947 85 :1@N1_:2@N7 29124 0.582 5.44 0.954 86 :1@C6_:2@N3 28706 0.574 4.92 1.02 87 :1@N1_:2@N3 28574 0.571 4.81 1.06 88 :1@N6_:2@C2 27667 0.553 4.8 1.08 89 :1@N6_:2@C5 27617 0.552 5.29 0.932 90 :1@N7_:2@C8 27539 0.551 5.51 0.878 91 :1@N7_:2@N9 27505 0.55 5.71 0.785 92 :1@N1_:2@N9 25320 0.506 5.28 0.904 93 :1@C6_:2@C8 25225 0.504 5.59 0.863 94 :1@C6_:2@N9 25046 0.501 5.44 0.84 95 :1@N1_:2@C8 24982 0.5 5.55 0.899 96 :1@N6_:2@N3 24472 0.489 5.09 0.979 97 :1@N6_:2@C4 24440 0.489 5.35 0.88 98 :1@N6_:2@N9 18955 0.379 5.81 0.699 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0026 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 50000 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 50000 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector), size is 50000 v_base2 "v_base2" (vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 34.7214 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.