CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/09/15 15:44:16 | Available memory: 89338.3 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 99 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@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@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@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: 31.8366 s TIME: Avg. throughput= 1570.5195 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 64.3601 99 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 37682 0.754 4.82 0.8 2 :1@N9_:2@C4 37512 0.75 5.1 0.732 3 :1@C4_:2@C5 37483 0.75 4.74 0.829 4 :1@N9_:2@N7 37461 0.749 4.85 0.928 5 :1@N9_:2@N9 37346 0.747 5.35 0.748 6 :1@N9_:2@C8 37302 0.746 5.14 0.917 7 :1@N3_:2@C5 37161 0.743 4.92 0.841 8 :1@C4_:2@C4 36909 0.738 4.94 0.833 9 :1@C4_:2@C6 36871 0.737 4.77 0.816 10 :1@N3_:2@C4 36761 0.735 4.96 0.887 11 :1@C4_:2@N7 36721 0.734 4.89 0.949 12 :1@N9_:2@C6 36572 0.731 4.93 0.855 13 :1@N3_:2@N7 36318 0.726 5.05 0.934 14 :1@N3_:2@C6 36281 0.726 5.05 0.88 15 :1@C5_:2@C6 35809 0.716 4.6 0.905 16 :1@C4_:2@N1 35767 0.715 4.97 0.879 17 :1@C4_:2@N6 35757 0.715 4.98 0.875 18 :1@C4_:2@N9 35645 0.713 5.22 0.895 19 :1@C4_:2@C8 35642 0.713 5.15 0.98 20 :1@C5_:2@C5 35610 0.712 4.79 0.954 21 :1@C8_:2@C5 35585 0.712 4.88 0.915 22 :1@N3_:2@N9 35422 0.708 5.11 0.976 23 :1@N3_:2@C8 35369 0.707 5.14 0.994 24 :1@C4_:2@N3 35369 0.707 5.14 0.864 25 :1@N9_:2@N3 35130 0.703 5.37 0.808 26 :1@C5_:2@N6 35099 0.702 4.65 0.929 27 :1@C4_:2@C2 35075 0.702 5.1 0.908 28 :1@C5_:2@N1 35051 0.701 4.72 0.936 29 :1@C8_:2@C6 35024 0.7 4.8 0.963 30 :1@N3_:2@N3 34921 0.698 5.1 0.918 31 :1@N9_:2@N6 34913 0.698 5.1 0.885 32 :1@C8_:2@C4 34769 0.695 5.29 0.81 33 :1@N3_:2@N1 34670 0.693 5.18 0.933 34 :1@N7_:2@C6 34546 0.691 4.64 0.97 35 :1@N3_:2@C2 34297 0.686 5.17 0.93 36 :1@C8_:2@N7 34286 0.686 4.92 1.03 37 :1@C2_:2@C5 34205 0.684 5.03 0.905 38 :1@C6_:2@C6 34115 0.682 4.72 0.959 39 :1@N7_:2@C5 34071 0.681 4.89 0.952 40 :1@C5_:2@C4 33999 0.68 5.05 0.936 41 :1@C2_:2@C6 33973 0.679 5.03 0.93 42 :1@N9_:2@N1 33876 0.678 5.14 0.892 43 :1@N3_:2@N6 33865 0.677 5.29 0.988 44 :1@C8_:2@N6 33859 0.677 4.78 1.02 45 :1@N7_:2@N6 33832 0.677 4.53 1.01 46 :1@C5_:2@C2 33678 0.674 4.95 0.992 47 :1@N7_:2@N1 33648 0.673 4.81 1.02 48 :1@C6_:2@N6 33600 0.672 4.76 0.99 49 :1@C5_:2@N7 33556 0.671 5.02 1.01 50 :1@C6_:2@N1 33519 0.67 4.68 0.974 51 :1@C2_:2@N1 33060 0.661 5.05 0.968 52 :1@N9_:2@C2 33008 0.66 5.27 0.899 53 :1@N1_:2@C6 32973 0.659 4.92 0.931 54 :1@C2_:2@C4 32929 0.659 4.97 0.992 55 :1@C6_:2@C5 32733 0.655 4.97 0.979 56 :1@C8_:2@N9 32726 0.655 5.61 0.784 57 :1@C8_:2@N1 32654 0.653 4.99 0.984 58 :1@N7_:2@C4 32627 0.653 5.31 0.877 59 :1@N1_:2@N1 32450 0.649 4.84 0.954 60 :1@C8_:2@C8 32444 0.649 5.32 0.934 61 :1@C2_:2@N7 32417 0.648 5.26 0.964 62 :1@C5_:2@N3 32338 0.647 5.12 0.952 63 :1@N1_:2@C5 32097 0.642 5.09 0.95 64 :1@N7_:2@N7 31971 0.639 5.05 1.04 65 :1@C2_:2@C2 31932 0.639 4.98 0.972 66 :1@C8_:2@N3 31789 0.636 5.47 0.864 67 :1@N7_:2@C2 31739 0.635 5.13 1.03 68 :1@N1_:2@N6 31549 0.631 5 1.02 69 :1@N6_:2@N6 31346 0.627 4.83 1.06 70 :1@C6_:2@C2 31251 0.625 4.78 1.03 71 :1@C2_:2@N3 31139 0.623 4.91 1.02 72 :1@C8_:2@C2 30987 0.62 5.24 0.963 73 :1@N6_:2@C6 30942 0.619 4.89 1.01 74 :1@N6_:2@N1 30782 0.616 4.72 1.05 75 :1@N7_:2@N3 30620 0.612 5.42 0.929 76 :1@N1_:2@C2 30453 0.609 4.79 1.01 77 :1@C5_:2@C8 30286 0.606 5.34 0.939 78 :1@C2_:2@C8 30269 0.605 5.32 0.979 79 :1@C2_:2@N9 30162 0.603 5.12 1.02 80 :1@C5_:2@N9 30093 0.602 5.39 0.878 81 :1@C6_:2@C4 30087 0.602 5.06 0.984 82 :1@N1_:2@C4 29955 0.599 5.03 1.02 83 :1@C6_:2@N7 29890 0.598 5.29 0.962 84 :1@N1_:2@N7 29346 0.587 5.42 0.968 85 :1@C6_:2@N3 28855 0.577 4.93 1.02 86 :1@N1_:2@N3 28619 0.572 4.84 1.06 87 :1@N7_:2@N9 27924 0.558 5.66 0.801 88 :1@N6_:2@C5 27858 0.557 5.25 0.947 89 :1@N6_:2@C2 27830 0.557 4.82 1.08 90 :1@N7_:2@C8 27788 0.556 5.44 0.893 91 :1@N1_:2@N9 25477 0.51 5.27 0.921 92 :1@C6_:2@C8 25467 0.509 5.54 0.882 93 :1@N1_:2@C8 25246 0.505 5.52 0.913 94 :1@C6_:2@N9 25214 0.504 5.4 0.86 95 :1@N6_:2@C4 24684 0.494 5.32 0.901 96 :1@N6_:2@N3 24618 0.492 5.09 0.994 97 :1@N6_:2@N7 23907 0.478 5.61 0.899 98 :1@N6_:2@N9 19336 0.387 5.76 0.724 99 :1@N6_:2@C8 18208 0.364 5.87 0.759 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 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: 32.5413 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.