CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/07/15 08:17:00 | Available memory: 80574.4 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,N2,C2,N3,C4,C5,C6,O6,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,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,N6,H61,H62,N7,C8,H8,N9 :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,N6,H61,H62,N7,C8,H8,N9 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,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,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. [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', 3302 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', 66 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*](42) Reference mask: [:1,2&!@H*](42) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :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,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 109 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@N2' 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@N2' 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@N2' 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@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@O6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N2' 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@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@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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 24.4335 s TIME: Avg. throughput= 2046.3668 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 75.5948 109 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 39964 0.799 5.06 0.732 2 :1@N9_:2@C5 39857 0.797 4.86 0.804 3 :1@C4_:2@C5 39729 0.795 4.74 0.813 4 :1@C4_:2@C4 39358 0.787 4.86 0.824 5 :1@N9_:2@N9 39355 0.787 5.33 0.763 6 :1@N3_:2@C5 39354 0.787 4.9 0.838 7 :1@C4_:2@C6 39233 0.785 4.76 0.79 8 :1@N3_:2@C4 39047 0.781 4.88 0.854 9 :1@N9_:2@C6 38850 0.777 4.95 0.832 10 :1@N9_:2@N7 38677 0.774 4.95 0.927 11 :1@C4_:2@N7 38565 0.771 4.99 0.926 12 :1@N3_:2@C6 38547 0.771 5.01 0.886 13 :1@N9_:2@N3 38430 0.769 5.26 0.792 14 :1@C4_:2@N1 38418 0.768 4.84 0.847 15 :1@N9_:2@C8 38399 0.768 5.19 0.917 16 :1@C4_:2@N3 38165 0.763 4.99 0.801 17 :1@C4_:2@O6 38133 0.763 5.05 0.827 18 :1@C5_:2@C6 38122 0.762 4.57 0.9 19 :1@N3_:2@N3 38065 0.761 4.98 0.851 20 :1@C4_:2@C2 37943 0.759 4.94 0.844 21 :1@N3_:2@N7 37909 0.758 5.12 0.908 22 :1@C5_:2@C5 37817 0.756 4.77 0.957 23 :1@C4_:2@N9 37708 0.754 5.19 0.894 24 :1@C5_:2@N1 37513 0.75 4.59 0.905 25 :1@N3_:2@N1 37477 0.75 5.04 0.941 26 :1@C8_:2@C5 37438 0.749 4.9 0.957 27 :1@N3_:2@C2 37426 0.749 5.02 0.895 28 :1@C5_:2@O6 37388 0.748 4.72 0.897 29 :1@N3_:2@N9 37307 0.746 5.07 0.954 30 :1@N9_:2@N1 37282 0.746 5.1 0.873 31 :1@C8_:2@C4 37171 0.743 5.25 0.856 32 :1@C8_:2@C6 37110 0.742 4.81 0.993 33 :1@C4_:2@C8 37038 0.741 5.19 0.962 34 :1@N9_:2@O6 36767 0.735 5.17 0.857 35 :1@N7_:2@C6 36756 0.735 4.62 1.02 36 :1@N9_:2@C2 36690 0.734 5.19 0.881 37 :1@N3_:2@C8 36446 0.729 5.15 0.959 38 :1@C5_:2@C2 36412 0.728 4.8 0.906 39 :1@C6_:2@C6 36394 0.728 4.66 0.949 40 :1@C5_:2@C4 36391 0.728 4.96 0.946 41 :1@N7_:2@N1 36308 0.726 4.73 1.04 42 :1@C2_:2@C6 36279 0.726 4.98 0.98 43 :1@C6_:2@O6 36196 0.724 4.81 1 44 :1@N3_:2@O6 36161 0.723 5.33 0.984 45 :1@C2_:2@N1 36128 0.723 4.93 0.986 46 :1@C6_:2@N1 36091 0.722 4.55 0.917 47 :1@N7_:2@C5 35980 0.72 4.88 0.996 48 :1@C2_:2@C5 35972 0.719 4.96 0.914 49 :1@C8_:2@N1 35826 0.717 4.97 0.985 50 :1@C2_:2@C4 35623 0.712 4.91 0.978 51 :1@C2_:2@C2 35620 0.712 4.9 0.927 52 :1@N7_:2@O6 35585 0.712 4.59 1.02 53 :1@N1_:2@N1 35507 0.71 4.74 0.942 54 :1@N1_:2@C6 35332 0.707 4.86 0.965 55 :1@C5_:2@N3 35327 0.707 5 0.899 56 :1@C8_:2@N3 35158 0.703 5.41 0.877 57 :1@C5_:2@N7 35134 0.703 5.07 0.965 58 :1@C2_:2@N3 35105 0.702 4.89 0.98 59 :1@C8_:2@O6 35099 0.702 4.82 1.02 60 :1@C8_:2@N7 35001 0.7 4.96 1.01 61 :1@N7_:2@C2 34816 0.696 5.04 1.01 62 :1@N7_:2@C4 34805 0.696 5.23 0.934 63 :1@C6_:2@C2 34646 0.693 4.7 0.952 64 :1@C6_:2@C5 34587 0.692 4.89 0.96 65 :1@C4_:2@N2 34557 0.691 5.29 0.916 66 :1@C8_:2@C2 34543 0.691 5.2 0.96 67 :1@N1_:2@C2 34364 0.687 4.77 0.969 68 :1@C8_:2@N9 34074 0.681 5.56 0.808 69 :1@C5_:2@N2 34008 0.68 5.11 0.924 70 :1@N1_:2@C5 33952 0.679 4.99 0.95 71 :1@N3_:2@N2 33921 0.678 5.34 0.996 72 :1@C2_:2@N7 33789 0.676 5.26 0.957 73 :1@N6_:2@O6 33731 0.675 4.87 1.09 74 :1@N6_:2@N1 33542 0.671 4.65 0.991 75 :1@N7_:2@N3 33503 0.67 5.32 0.931 76 :1@N1_:2@O6 33378 0.668 4.99 1.06 77 :1@N6_:2@C6 33285 0.666 4.83 0.998 78 :1@C8_:2@C8 33238 0.665 5.34 0.912 79 :1@C2_:2@N2 33015 0.66 5.13 0.95 80 :1@C6_:2@N2 33013 0.66 4.91 0.96 81 :1@N7_:2@N7 32896 0.658 5.07 0.996 82 :1@N1_:2@C4 32817 0.656 4.99 1.01 83 :1@C2_:2@O6 32808 0.656 5.14 1.1 84 :1@C6_:2@C4 32755 0.655 4.99 0.971 85 :1@C6_:2@N3 32557 0.651 4.91 0.989 86 :1@N1_:2@N3 32545 0.651 4.87 1.05 87 :1@C2_:2@N9 32247 0.645 5.09 1.01 88 :1@N1_:2@N2 32232 0.645 4.91 0.938 89 :1@C5_:2@N9 32116 0.642 5.33 0.888 90 :1@C2_:2@C8 31698 0.634 5.3 0.96 91 :1@C5_:2@C8 31546 0.631 5.33 0.9 92 :1@N6_:2@C2 31500 0.63 4.82 1.06 93 :1@C6_:2@N7 31445 0.629 5.28 0.928 94 :1@N1_:2@N7 30866 0.617 5.38 0.976 95 :1@N9_:2@N2 30433 0.609 5.4 0.941 96 :1@N7_:2@N2 30332 0.607 5.21 1.01 97 :1@N6_:2@N2 30062 0.601 4.85 1.13 98 :1@N6_:2@C5 29994 0.6 5.18 0.929 99 :1@N7_:2@N9 29279 0.586 5.57 0.833 100 :1@N7_:2@C8 29057 0.581 5.44 0.868 101 :1@C8_:2@N2 28712 0.574 5.35 1.01 102 :1@N6_:2@N3 27992 0.56 5.11 1 103 :1@N1_:2@N9 27614 0.552 5.23 0.906 104 :1@C6_:2@C8 27503 0.55 5.52 0.865 105 :1@C6_:2@N9 27478 0.55 5.35 0.852 106 :1@N6_:2@C4 27141 0.543 5.26 0.876 107 :1@N1_:2@C8 27119 0.542 5.49 0.914 108 :1@N6_:2@N7 25809 0.516 5.59 0.915 109 :1@N6_:2@C8 20336 0.407 5.85 0.809 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: 25.1271 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.