CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 17:40:52 | Available memory: 79535.2 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, 48713 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 48713 of 48713) Looking for frames at 396.40 K Coordinate processing will occur on 48713 frames. TIME: Run Initialization took 0.0003 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 (1-48713, 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 88 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@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@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@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@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@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@C2' to ':2@C6' 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@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N3' to ':2@N9' 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 48713 frames and processed 48713 frames. TIME: Trajectory processing: 59.6057 s TIME: Avg. throughput= 817.2540 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 67.4283 88 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 41158 0.845 4.7 0.763 2 :1@N9_:2@C4 41066 0.843 4.88 0.701 3 :1@C4_:2@C5 40899 0.84 4.57 0.795 4 :1@N9_:2@N9 40710 0.836 5.17 0.735 5 :1@C4_:2@C4 40556 0.833 4.71 0.798 6 :1@C4_:2@C6 40436 0.83 4.61 0.797 7 :1@N9_:2@N7 40428 0.83 4.82 0.896 8 :1@N3_:2@C5 40395 0.829 4.79 0.792 9 :1@N9_:2@C6 40301 0.827 4.82 0.815 10 :1@N3_:2@C4 40294 0.827 4.78 0.814 11 :1@N9_:2@C8 40109 0.823 5.06 0.908 12 :1@C4_:2@N7 39916 0.819 4.84 0.904 13 :1@N9_:2@N3 39788 0.817 5.13 0.793 14 :1@N3_:2@C6 39775 0.817 4.94 0.878 15 :1@C4_:2@N1 39689 0.815 4.73 0.852 16 :1@C4_:2@N3 39497 0.811 4.87 0.772 17 :1@C5_:2@C6 39473 0.81 4.39 0.872 18 :1@C4_:2@O6 39456 0.81 4.92 0.849 19 :1@C8_:2@C5 39439 0.81 4.77 0.881 20 :1@N3_:2@N3 39310 0.807 4.92 0.814 21 :1@C5_:2@C5 39275 0.806 4.6 0.92 22 :1@C4_:2@N9 39237 0.805 5.05 0.878 23 :1@C4_:2@C2 39215 0.805 4.84 0.817 24 :1@C8_:2@C4 39196 0.805 5.11 0.793 25 :1@C8_:2@C6 39138 0.803 4.69 0.937 26 :1@N3_:2@N1 39017 0.801 5.02 0.939 27 :1@C5_:2@N1 38897 0.798 4.44 0.864 28 :1@N3_:2@N9 38845 0.797 4.98 0.934 29 :1@N3_:2@C2 38829 0.797 5.01 0.861 30 :1@N9_:2@O6 38824 0.797 5.1 0.843 31 :1@C5_:2@O6 38786 0.796 4.53 0.897 32 :1@N7_:2@C6 38645 0.793 4.46 0.941 33 :1@C4_:2@C8 38596 0.792 5.05 0.946 34 :1@N9_:2@N1 38450 0.789 4.97 0.877 35 :1@N7_:2@N1 38263 0.785 4.59 1.01 36 :1@C5_:2@C4 38141 0.783 4.84 0.885 37 :1@N7_:2@C5 38090 0.782 4.73 0.907 38 :1@C5_:2@C2 37990 0.78 4.68 0.858 39 :1@N9_:2@C2 37952 0.779 5.07 0.888 40 :1@N7_:2@O6 37697 0.774 4.46 0.952 41 :1@C8_:2@N1 37676 0.773 4.84 0.984 42 :1@C8_:2@O6 37672 0.773 4.77 0.976 43 :1@C6_:2@C6 37668 0.773 4.51 0.926 44 :1@C8_:2@N7 37616 0.772 4.88 0.991 45 :1@C2_:2@C4 37601 0.772 4.92 0.921 46 :1@C2_:2@C6 37542 0.771 4.94 0.927 47 :1@C2_:2@N1 37533 0.77 4.94 0.941 48 :1@C6_:2@N1 37479 0.769 4.44 0.87 49 :1@C6_:2@O6 37437 0.769 4.6 1.03 50 :1@N3_:2@O6 37383 0.767 5.26 1 51 :1@C5_:2@N3 37344 0.767 4.91 0.857 52 :1@N7_:2@C4 37292 0.766 5.13 0.849 53 :1@C8_:2@N3 37282 0.765 5.29 0.871 54 :1@C2_:2@C2 37117 0.762 4.94 0.894 55 :1@C8_:2@N9 37114 0.762 5.48 0.759 56 :1@N1_:2@N1 36993 0.759 4.69 0.893 57 :1@C5_:2@N7 36885 0.757 4.92 0.951 58 :1@C2_:2@N3 36873 0.757 4.92 0.958 59 :1@N1_:2@C6 36845 0.756 4.76 0.926 60 :1@N7_:2@C2 36782 0.755 4.92 0.993 61 :1@C6_:2@C2 36592 0.751 4.68 0.942 62 :1@C8_:2@C2 36389 0.747 5.07 0.985 63 :1@C6_:2@C5 36252 0.744 4.81 0.938 64 :1@N1_:2@C2 36209 0.743 4.78 0.955 65 :1@C8_:2@C8 36067 0.74 5.27 0.908 66 :1@C4_:2@N2 36030 0.74 5.24 0.869 67 :1@N7_:2@N3 35902 0.737 5.22 0.883 68 :1@C5_:2@N2 35760 0.734 5.04 0.903 69 :1@N7_:2@N7 35746 0.734 4.99 0.986 70 :1@O6_:2@N1 35722 0.733 4.58 0.965 71 :1@N3_:2@N2 35370 0.726 5.37 0.952 72 :1@O6_:2@C6 35114 0.721 4.7 0.946 73 :1@N1_:2@O6 35043 0.719 4.86 1.09 74 :1@O6_:2@O6 35025 0.719 4.64 1.06 75 :1@C6_:2@N2 34964 0.718 4.92 1 76 :1@C6_:2@N3 34937 0.717 4.96 0.995 77 :1@N1_:2@N3 34722 0.713 4.92 1.06 78 :1@C2_:2@N2 34171 0.701 5.18 0.957 79 :1@O6_:2@C2 34010 0.698 4.86 1.07 80 :1@N1_:2@N2 33941 0.697 4.95 0.994 81 :1@N2_:2@N3 33564 0.689 5.16 0.987 82 :1@N2_:2@C2 33376 0.685 5.25 0.97 83 :1@N2_:2@N1 32744 0.672 5.3 1.02 84 :1@N7_:2@N2 32226 0.662 5.1 1.03 85 :1@N9_:2@N2 32107 0.659 5.35 0.939 86 :1@O6_:2@N2 31709 0.651 4.88 1.16 87 :1@C8_:2@N2 30349 0.623 5.23 1.06 88 :1@N2_:2@N2 28683 0.589 5.23 1.02 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0026 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 48713 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 48713 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 48713 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 48713 COM "COM" (double, distance), size is 48713 v_base1 "v_base1" (vector), size is 48713 v_base2 "v_base2" (vector), size is 48713 normalangle "normalangle" (double), size is 48713 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: 61.1949 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.