CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 19:21:02 | Available memory: 87102.9 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 0.0080 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 102 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@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@C4' 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@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@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@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@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@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: 36.0456 s TIME: Avg. throughput= 1387.1310 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 74.6663 102 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 40968 0.819 4.76 0.778 2 :1@N9_:2@C4 40963 0.819 4.94 0.712 3 :1@C4_:2@C5 40773 0.815 4.62 0.801 4 :1@N9_:2@N9 40713 0.814 5.2 0.741 5 :1@C4_:2@C4 40521 0.81 4.74 0.803 6 :1@N3_:2@C5 40261 0.805 4.82 0.795 7 :1@N3_:2@C4 40225 0.804 4.8 0.817 8 :1@N9_:2@N7 40200 0.804 4.85 0.907 9 :1@C4_:2@C6 40194 0.804 4.68 0.803 10 :1@N9_:2@C8 39989 0.8 5.07 0.916 11 :1@N9_:2@C6 39941 0.799 4.91 0.836 12 :1@C4_:2@N7 39822 0.796 4.87 0.913 13 :1@N3_:2@C6 39535 0.791 4.97 0.881 14 :1@N9_:2@N3 39395 0.788 5.18 0.797 15 :1@C4_:2@N3 39380 0.788 4.9 0.782 16 :1@C4_:2@N1 39370 0.787 4.79 0.863 17 :1@C4_:2@N9 39359 0.787 5.07 0.884 18 :1@C5_:2@C6 39239 0.785 4.45 0.876 19 :1@N3_:2@N3 39239 0.785 4.92 0.823 20 :1@C8_:2@C5 39174 0.783 4.82 0.891 21 :1@C5_:2@C5 39104 0.782 4.63 0.921 22 :1@C4_:2@O6 39099 0.782 4.99 0.853 23 :1@N3_:2@N7 39019 0.78 5.05 0.876 24 :1@C8_:2@C4 38964 0.779 5.16 0.799 25 :1@C4_:2@C2 38894 0.778 4.87 0.83 26 :1@N3_:2@N9 38887 0.778 5 0.939 27 :1@N3_:2@N1 38746 0.775 5.03 0.952 28 :1@C5_:2@N1 38654 0.773 4.51 0.877 29 :1@C8_:2@C6 38623 0.772 4.78 0.952 30 :1@C4_:2@C8 38621 0.772 5.06 0.957 31 :1@N3_:2@C2 38617 0.772 5 0.879 32 :1@C5_:2@O6 38414 0.768 4.61 0.899 33 :1@N7_:2@C6 38391 0.768 4.55 0.959 34 :1@N9_:2@O6 38034 0.761 5.17 0.852 35 :1@N3_:2@C8 37992 0.76 5.09 0.941 36 :1@C5_:2@C4 37971 0.759 4.85 0.885 37 :1@N7_:2@N1 37861 0.757 4.7 1.02 38 :1@N7_:2@C5 37854 0.757 4.77 0.912 39 :1@C5_:2@C2 37777 0.756 4.74 0.868 40 :1@N9_:2@N1 37776 0.756 5.05 0.885 41 :1@C2_:2@C4 37563 0.751 4.9 0.924 42 :1@C2_:2@C5 37557 0.751 4.93 0.855 43 :1@C6_:2@C6 37474 0.749 4.54 0.929 44 :1@C2_:2@N1 37328 0.747 4.91 0.95 45 :1@N9_:2@C2 37319 0.746 5.13 0.893 46 :1@C8_:2@N7 37311 0.746 4.89 0.988 47 :1@C2_:2@C6 37282 0.746 4.93 0.927 48 :1@C6_:2@N1 37259 0.745 4.47 0.873 49 :1@C5_:2@N3 37214 0.744 4.94 0.864 50 :1@C6_:2@O6 37182 0.744 4.65 1.03 51 :1@N7_:2@O6 37107 0.742 4.54 0.962 52 :1@C2_:2@C2 37091 0.742 4.89 0.898 53 :1@N7_:2@C4 37060 0.741 5.15 0.857 54 :1@N3_:2@O6 37014 0.74 5.3 0.996 55 :1@C8_:2@N1 36932 0.739 4.94 0.993 56 :1@C8_:2@N9 36927 0.739 5.48 0.763 57 :1@C8_:2@O6 36882 0.738 4.85 0.986 58 :1@C2_:2@N3 36859 0.737 4.88 0.952 59 :1@C5_:2@N7 36854 0.737 4.93 0.956 60 :1@N1_:2@N1 36838 0.737 4.67 0.894 61 :1@C8_:2@N3 36822 0.736 5.34 0.871 62 :1@N1_:2@C6 36740 0.735 4.76 0.936 63 :1@C6_:2@C2 36468 0.729 4.69 0.94 64 :1@N7_:2@C2 36338 0.727 5 0.997 65 :1@N1_:2@C2 36179 0.724 4.75 0.943 66 :1@C6_:2@C5 36105 0.722 4.81 0.941 67 :1@N1_:2@C5 36003 0.72 4.95 0.933 68 :1@C8_:2@C8 35944 0.719 5.25 0.902 69 :1@C8_:2@C2 35638 0.713 5.15 0.98 70 :1@N7_:2@N7 35558 0.711 4.98 0.982 71 :1@O6_:2@N1 35539 0.711 4.61 0.975 72 :1@N7_:2@N3 35507 0.71 5.26 0.888 73 :1@C4_:2@N2 35439 0.709 5.26 0.882 74 :1@C2_:2@N7 35427 0.709 5.24 0.945 75 :1@C5_:2@N2 35355 0.707 5.1 0.909 76 :1@N1_:2@C4 35165 0.703 4.99 0.992 77 :1@N2_:2@C4 35025 0.701 5.23 0.936 78 :1@C6_:2@C4 34910 0.698 4.99 0.947 79 :1@O6_:2@C6 34904 0.698 4.71 0.952 80 :1@C5_:2@N9 34888 0.698 5.28 0.871 81 :1@N1_:2@O6 34836 0.697 4.87 1.07 82 :1@O6_:2@O6 34649 0.693 4.67 1.05 83 :1@C2_:2@N9 34442 0.689 5.12 0.985 84 :1@C5_:2@C8 34412 0.688 5.26 0.923 85 :1@N2_:2@C5 34306 0.686 5.33 0.888 86 :1@C2_:2@O6 34055 0.681 5.11 1.09 87 :1@C2_:2@C8 33610 0.672 5.31 0.955 88 :1@C6_:2@N7 33523 0.67 5.22 0.959 89 :1@N7_:2@N9 33037 0.661 5.55 0.802 90 :1@N2_:2@N1 32896 0.658 5.23 1.04 91 :1@O6_:2@C5 32624 0.652 5.14 0.925 92 :1@N1_:2@N7 32620 0.652 5.31 0.977 93 :1@N2_:2@C6 32405 0.648 5.27 0.99 94 :1@N7_:2@C8 32305 0.646 5.37 0.872 95 :1@N7_:2@N2 31314 0.626 5.19 1.03 96 :1@N2_:2@N9 31088 0.622 5.27 0.973 97 :1@N9_:2@N2 31056 0.621 5.37 0.938 98 :1@N2_:2@N7 30253 0.605 5.49 0.99 99 :1@N2_:2@C8 29663 0.593 5.52 0.961 100 :1@N1_:2@C8 29399 0.588 5.5 0.938 101 :1@C8_:2@N2 29160 0.583 5.3 1.04 102 :1@N2_:2@O6 26094 0.522 5.18 1.16 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0334 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: 37.4745 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.