CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 19:47:16 | Available memory: 90101.1 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,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :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,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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', 3303 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 0.0001 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', 67 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 118 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@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@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@O6' to ':2@C8' Atom ':1@O6' to ':2@N7' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@N2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' 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@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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: 32.4187 s TIME: Avg. throughput= 1542.3186 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 85.5181 118 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 41394 0.828 4.75 0.781 2 :1@N9_:2@C4 41314 0.826 4.93 0.713 3 :1@C4_:2@C5 41127 0.823 4.61 0.814 4 :1@N9_:2@N9 41011 0.82 5.2 0.747 5 :1@C4_:2@C4 40862 0.817 4.74 0.813 6 :1@N3_:2@C5 40664 0.813 4.81 0.809 7 :1@N3_:2@C4 40590 0.812 4.78 0.827 8 :1@N9_:2@N7 40580 0.812 4.83 0.911 9 :1@C4_:2@C6 40541 0.811 4.66 0.803 10 :1@N9_:2@C6 40404 0.808 4.9 0.818 11 :1@N9_:2@C8 40213 0.804 5.06 0.908 12 :1@C4_:2@N7 40055 0.801 4.85 0.916 13 :1@N3_:2@C6 39922 0.798 4.96 0.88 14 :1@N9_:2@N3 39881 0.798 5.19 0.794 15 :1@C4_:2@N1 39870 0.797 4.78 0.849 16 :1@C4_:2@N3 39725 0.794 4.89 0.78 17 :1@N3_:2@N3 39686 0.794 4.89 0.825 18 :1@C4_:2@N9 39565 0.791 5.06 0.881 19 :1@C5_:2@C6 39524 0.79 4.43 0.895 20 :1@C8_:2@C5 39424 0.788 4.81 0.894 21 :1@C4_:2@C2 39423 0.788 4.87 0.821 22 :1@C4_:2@O6 39410 0.788 4.97 0.851 23 :1@N3_:2@N7 39314 0.786 5.04 0.879 24 :1@C5_:2@C5 39243 0.785 4.62 0.93 25 :1@N3_:2@N1 39199 0.784 5.02 0.934 26 :1@N3_:2@N9 39142 0.783 4.98 0.934 27 :1@N3_:2@C2 39136 0.783 4.98 0.865 28 :1@C8_:2@C4 39036 0.781 5.16 0.805 29 :1@C8_:2@C6 39000 0.78 4.76 0.942 30 :1@C5_:2@N1 38988 0.78 4.5 0.88 31 :1@C4_:2@C8 38829 0.777 5.06 0.947 32 :1@N9_:2@O6 38656 0.773 5.16 0.84 33 :1@C5_:2@O6 38655 0.773 4.57 0.914 34 :1@N7_:2@C6 38591 0.772 4.53 0.965 35 :1@N9_:2@N1 38523 0.77 5.07 0.87 36 :1@N3_:2@C8 38372 0.767 5.09 0.935 37 :1@C5_:2@C2 38153 0.763 4.74 0.874 38 :1@N7_:2@N1 38125 0.762 4.68 1.01 39 :1@C5_:2@C4 38098 0.762 4.84 0.886 40 :1@N9_:2@C2 37954 0.759 5.16 0.884 41 :1@N7_:2@C5 37919 0.758 4.75 0.919 42 :1@C2_:2@N1 37747 0.755 4.89 0.948 43 :1@C2_:2@C4 37737 0.755 4.87 0.924 44 :1@C2_:2@C5 37707 0.754 4.91 0.859 45 :1@C2_:2@C6 37678 0.754 4.92 0.937 46 :1@C6_:2@C6 37635 0.753 4.51 0.944 47 :1@C2_:2@C2 37565 0.751 4.86 0.902 48 :1@C6_:2@N1 37522 0.75 4.44 0.891 49 :1@C5_:2@N3 37503 0.75 4.94 0.87 50 :1@C8_:2@N1 37457 0.749 4.95 0.978 51 :1@N3_:2@O6 37451 0.749 5.3 0.994 52 :1@C8_:2@N7 37447 0.749 4.86 0.981 53 :1@N7_:2@O6 37441 0.749 4.5 0.971 54 :1@C8_:2@O6 37390 0.748 4.82 0.976 55 :1@C6_:2@O6 37300 0.746 4.62 1.04 56 :1@C2_:2@N3 37206 0.744 4.84 0.956 57 :1@N1_:2@N1 37150 0.743 4.65 0.905 58 :1@N7_:2@C4 37138 0.743 5.15 0.862 59 :1@C8_:2@N3 36912 0.738 5.36 0.875 60 :1@N1_:2@C6 36877 0.738 4.74 0.937 61 :1@C8_:2@N9 36867 0.737 5.48 0.761 62 :1@C5_:2@N7 36863 0.737 4.92 0.952 63 :1@C6_:2@C2 36783 0.736 4.67 0.954 64 :1@N7_:2@C2 36597 0.732 5.01 0.997 65 :1@N1_:2@C2 36567 0.731 4.72 0.957 66 :1@C6_:2@C5 36186 0.724 4.8 0.943 67 :1@C4_:2@N2 36146 0.723 5.28 0.875 68 :1@C8_:2@C8 36097 0.722 5.25 0.893 69 :1@N1_:2@C5 36077 0.722 4.94 0.927 70 :1@C8_:2@C2 35937 0.719 5.17 0.976 71 :1@N3_:2@N2 35886 0.718 5.34 0.949 72 :1@C5_:2@N2 35742 0.715 5.09 0.909 73 :1@O6_:2@N1 35697 0.714 4.57 0.992 74 :1@N7_:2@N3 35570 0.711 5.27 0.892 75 :1@N7_:2@N7 35509 0.71 4.96 0.972 76 :1@N1_:2@C4 35439 0.709 4.98 0.99 77 :1@C2_:2@N7 35437 0.709 5.23 0.932 78 :1@N1_:2@N3 35256 0.705 4.86 1.05 79 :1@C6_:2@N3 35239 0.705 4.95 0.996 80 :1@C6_:2@N2 35201 0.704 4.92 1 81 :1@N2_:2@C4 35154 0.703 5.18 0.938 82 :1@N1_:2@O6 35088 0.702 4.87 1.08 83 :1@C6_:2@C4 35054 0.701 4.98 0.944 84 :1@C5_:2@N9 34946 0.699 5.29 0.863 85 :1@O6_:2@C6 34932 0.699 4.68 0.96 86 :1@C2_:2@N2 34858 0.697 5.1 0.937 87 :1@O6_:2@O6 34853 0.697 4.64 1.07 88 :1@C2_:2@N9 34796 0.696 5.11 0.983 89 :1@N1_:2@N2 34597 0.692 4.89 0.983 90 :1@C5_:2@C8 34470 0.689 5.27 0.91 91 :1@N2_:2@C5 34461 0.689 5.31 0.887 92 :1@C2_:2@O6 34420 0.688 5.12 1.09 93 :1@N2_:2@N3 34409 0.688 5.05 0.995 94 :1@N2_:2@C2 34164 0.683 5.13 0.97 95 :1@O6_:2@C2 34132 0.683 4.85 1.08 96 :1@C2_:2@C8 33787 0.676 5.32 0.941 97 :1@C6_:2@N7 33439 0.669 5.22 0.943 98 :1@N2_:2@N1 33408 0.668 5.22 1.04 99 :1@N7_:2@N9 33016 0.66 5.56 0.795 100 :1@N1_:2@N7 32645 0.653 5.32 0.96 101 :1@N2_:2@C6 32644 0.653 5.27 0.991 102 :1@O6_:2@C5 32540 0.651 5.13 0.913 103 :1@N7_:2@C8 32333 0.647 5.39 0.857 104 :1@O6_:2@N2 31872 0.637 4.88 1.16 105 :1@N9_:2@N2 31419 0.628 5.41 0.937 106 :1@N2_:2@N9 31319 0.626 5.25 0.972 107 :1@N1_:2@N9 30517 0.61 5.31 0.921 108 :1@N2_:2@N2 30498 0.61 5.15 1 109 :1@O6_:2@C4 30434 0.609 5.35 0.903 110 :1@O6_:2@N3 30387 0.608 5.18 1 111 :1@N2_:2@N7 30341 0.607 5.5 0.977 112 :1@C6_:2@N9 30115 0.602 5.44 0.865 113 :1@C6_:2@C8 29812 0.596 5.56 0.895 114 :1@N2_:2@C8 29745 0.595 5.52 0.948 115 :1@N1_:2@C8 29511 0.59 5.53 0.918 116 :1@O6_:2@N7 28224 0.564 5.55 0.932 117 :1@N2_:2@O6 26221 0.524 5.2 1.16 118 :1@O6_:2@C8 21268 0.425 5.83 0.815 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0027 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: 33.0918 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.