CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/03/15 13:06:54 | Available memory: 79821.7 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,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', 4378 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 49121 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 49121 of 49121) Looking for frames at 396.40 K Coordinate processing will occur on 49121 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 4311 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 (1-49121, 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 119 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@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@O6' to ':2@N9' 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@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 49121 frames and processed 49121 frames. TIME: Trajectory processing: 64.6756 s TIME: Avg. throughput= 759.4986 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 86.9673 119 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C4 41073 0.836 4.92 0.701 2 :1@N9_:2@C5 41046 0.836 4.74 0.762 3 :1@C4_:2@C5 40741 0.829 4.59 0.793 4 :1@N9_:2@N9 40545 0.825 5.18 0.74 5 :1@C4_:2@C4 40423 0.823 4.72 0.803 6 :1@C4_:2@C6 40379 0.822 4.65 0.8 7 :1@N9_:2@C6 40273 0.82 4.89 0.831 8 :1@N3_:2@C5 40196 0.818 4.79 0.789 9 :1@N9_:2@N7 40046 0.815 4.84 0.9 10 :1@N3_:2@C4 39960 0.814 4.77 0.811 11 :1@N9_:2@N3 39764 0.81 5.17 0.803 12 :1@C4_:2@N1 39707 0.808 4.77 0.87 13 :1@N9_:2@C8 39667 0.808 5.06 0.92 14 :1@C4_:2@N7 39645 0.807 4.83 0.909 15 :1@N3_:2@C6 39600 0.806 4.94 0.876 16 :1@C5_:2@C6 39406 0.802 4.41 0.87 17 :1@C4_:2@N3 39388 0.802 4.9 0.775 18 :1@C8_:2@C5 39382 0.802 4.82 0.884 19 :1@C4_:2@O6 39335 0.801 4.95 0.855 20 :1@C4_:2@C2 39240 0.799 4.87 0.836 21 :1@C8_:2@C4 39214 0.798 5.16 0.798 22 :1@C8_:2@C6 39119 0.796 4.77 0.945 23 :1@C5_:2@C5 39088 0.796 4.6 0.922 24 :1@N3_:2@N3 39050 0.795 4.91 0.812 25 :1@C4_:2@N9 38953 0.793 5.04 0.892 26 :1@N3_:2@N7 38928 0.792 5.01 0.878 27 :1@N3_:2@N1 38918 0.792 5.01 0.951 28 :1@C5_:2@N1 38896 0.792 4.49 0.876 29 :1@C5_:2@O6 38730 0.788 4.56 0.895 30 :1@N7_:2@C6 38656 0.787 4.53 0.95 31 :1@N3_:2@C2 38649 0.787 4.99 0.87 32 :1@N9_:2@O6 38532 0.784 5.17 0.855 33 :1@N3_:2@N9 38511 0.784 4.97 0.954 34 :1@C4_:2@C8 38303 0.78 5.03 0.966 35 :1@N7_:2@N1 38225 0.778 4.68 1.03 36 :1@N9_:2@N1 38195 0.778 5.02 0.898 37 :1@N7_:2@C5 37910 0.772 4.75 0.911 38 :1@C5_:2@C2 37869 0.771 4.74 0.863 39 :1@C5_:2@C4 37853 0.771 4.84 0.889 40 :1@N3_:2@C8 37756 0.769 5.05 0.952 41 :1@N9_:2@C2 37649 0.766 5.11 0.906 42 :1@N7_:2@O6 37635 0.766 4.52 0.96 43 :1@C2_:2@C5 37596 0.765 4.89 0.856 44 :1@C6_:2@C6 37582 0.765 4.48 0.921 45 :1@C2_:2@C6 37537 0.764 4.9 0.917 46 :1@C6_:2@O6 37470 0.763 4.58 1.02 47 :1@C2_:2@N1 37467 0.763 4.91 0.938 48 :1@C8_:2@O6 37443 0.762 4.86 0.976 49 :1@C8_:2@N1 37352 0.76 4.92 0.998 50 :1@C6_:2@N1 37346 0.76 4.44 0.861 51 :1@N3_:2@O6 37335 0.76 5.27 1.01 52 :1@C8_:2@N7 37306 0.759 4.88 0.999 53 :1@C2_:2@C4 37300 0.759 4.88 0.929 54 :1@C5_:2@N3 37150 0.756 4.95 0.857 55 :1@N7_:2@C4 37133 0.756 5.15 0.856 56 :1@C8_:2@N3 37007 0.753 5.33 0.874 57 :1@C2_:2@C2 36980 0.753 4.9 0.891 58 :1@N1_:2@N1 36946 0.752 4.66 0.886 59 :1@N1_:2@C6 36944 0.752 4.72 0.923 60 :1@C8_:2@N9 36856 0.75 5.48 0.761 61 :1@C5_:2@N7 36828 0.75 4.89 0.967 62 :1@C2_:2@N3 36607 0.745 4.89 0.956 63 :1@N7_:2@C2 36500 0.743 4.99 1 64 :1@C6_:2@C2 36462 0.742 4.7 0.939 65 :1@C6_:2@C5 36138 0.736 4.77 0.952 66 :1@N1_:2@C2 36106 0.735 4.77 0.954 67 :1@N1_:2@C5 36093 0.735 4.91 0.941 68 :1@C8_:2@C2 35915 0.731 5.12 0.994 69 :1@C8_:2@C8 35706 0.727 5.24 0.916 70 :1@O6_:2@N1 35662 0.726 4.58 0.972 71 :1@C4_:2@N2 35653 0.726 5.26 0.892 72 :1@N7_:2@N3 35625 0.725 5.27 0.884 73 :1@C2_:2@N7 35527 0.723 5.18 0.963 74 :1@N7_:2@N7 35467 0.722 4.95 0.996 75 :1@C5_:2@N2 35411 0.721 5.1 0.912 76 :1@N1_:2@O6 35351 0.72 4.82 1.07 77 :1@N3_:2@N2 35276 0.718 5.36 0.972 78 :1@O6_:2@O6 35187 0.716 4.6 1.05 79 :1@O6_:2@C6 35062 0.714 4.65 0.953 80 :1@N1_:2@C4 34949 0.711 4.97 1.01 81 :1@N2_:2@C4 34795 0.708 5.21 0.943 82 :1@C6_:2@N3 34723 0.707 4.97 0.999 83 :1@C6_:2@N2 34713 0.707 4.97 0.989 84 :1@C6_:2@C4 34672 0.706 4.97 0.961 85 :1@C5_:2@N9 34596 0.704 5.27 0.889 86 :1@C2_:2@O6 34573 0.704 5.08 1.09 87 :1@N1_:2@N3 34513 0.703 4.9 1.06 88 :1@N2_:2@C5 34469 0.702 5.31 0.888 89 :1@C5_:2@C8 34140 0.695 5.23 0.941 90 :1@C2_:2@N9 34063 0.693 5.08 1.01 91 :1@C2_:2@N2 34057 0.693 5.16 0.952 92 :1@N1_:2@N2 33832 0.689 4.96 0.985 93 :1@O6_:2@C2 33791 0.688 4.89 1.08 94 :1@C6_:2@N7 33619 0.684 5.17 0.975 95 :1@N2_:2@C2 33585 0.684 5.19 0.974 96 :1@N2_:2@N3 33575 0.684 5.11 0.995 97 :1@C2_:2@C8 33420 0.68 5.26 0.979 98 :1@N2_:2@N1 33075 0.673 5.25 1.02 99 :1@N1_:2@N7 32846 0.669 5.25 0.998 100 :1@N7_:2@N9 32796 0.668 5.55 0.801 101 :1@N2_:2@C6 32731 0.666 5.27 0.971 102 :1@O6_:2@C5 32654 0.665 5.09 0.941 103 :1@N7_:2@C8 31953 0.65 5.35 0.884 104 :1@O6_:2@N2 31368 0.639 4.94 1.15 105 :1@N7_:2@N2 31277 0.637 5.15 1.04 106 :1@N2_:2@N9 30562 0.622 5.22 0.991 107 :1@N2_:2@N7 30443 0.62 5.44 1.01 108 :1@O6_:2@C4 29933 0.609 5.32 0.925 109 :1@O6_:2@N3 29727 0.605 5.19 1.02 110 :1@N1_:2@N9 29701 0.605 5.26 0.952 111 :1@C6_:2@C8 29638 0.603 5.49 0.931 112 :1@N2_:2@C8 29462 0.6 5.45 0.982 113 :1@C6_:2@N9 29373 0.598 5.38 0.89 114 :1@C8_:2@N2 29318 0.597 5.24 1.07 115 :1@N1_:2@C8 29288 0.596 5.45 0.96 116 :1@N2_:2@N2 29067 0.592 5.19 1.02 117 :1@O6_:2@N7 28549 0.581 5.49 0.967 118 :1@O6_:2@N9 22738 0.463 5.72 0.754 119 :1@O6_:2@C8 21556 0.439 5.75 0.838 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 49121 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 49121 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 49121 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 49121 COM "COM" (double, distance), size is 49121 v_base1 "v_base1" (vector), size is 49121 v_base2 "v_base2" (vector), size is 49121 normalangle "normalangle" (double), size is 49121 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: 65.7054 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.