CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:35:13 | Available memory: 6121.49 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c4] Reading '../ctraj.c4' as Amber NetCDF [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,C2,N3,C4,C5,C6,N6,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,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9] 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,N6,H61,H62,N7,C8,H8,N9, 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,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 9730 frames INPUT TRAJECTORIES: 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 9730 of 9730) Coordinate processing will occur on 9730 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 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*](41) Reference mask: [:1,2&!@H*](41) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9] :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,N6,H61,H62,N7,C8,H8,N9 (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,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c4 (1-9730, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 90 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@N6' 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@N6' 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@N6' 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@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' 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@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' 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@N6' Atom ':1@N1' to ':2@N1' 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@N6' 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@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@N6' 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@N6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 9730 frames and processed 9730 frames. TIME: Trajectory processing: 0.7175 s TIME: Avg. throughput= 13560.9000 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 59.0872 90 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@C6 8375 0.861 4.49 0.932 2 :1@N3_:2@N6 8313 0.854 4.46 0.992 3 :1@N9_:2@C5 8272 0.85 5.27 0.734 4 :1@N3_:2@N1 8267 0.85 4.53 0.92 5 :1@N3_:2@C5 8232 0.846 4.89 0.848 6 :1@C4_:2@C6 8181 0.841 4.77 0.872 7 :1@N9_:2@N7 8179 0.841 5.46 0.638 8 :1@N9_:2@C6 8141 0.837 5.09 0.789 9 :1@C4_:2@N6 8112 0.834 4.65 0.86 10 :1@N3_:2@C2 8043 0.827 4.91 0.894 11 :1@C4_:2@N1 8041 0.826 4.88 0.98 12 :1@C2_:2@N1 8034 0.826 4.54 0.998 13 :1@N9_:2@N6 8026 0.825 5.11 0.735 14 :1@C4_:2@C5 8026 0.825 5.15 0.759 15 :1@C2_:2@C6 7958 0.818 4.57 0.933 16 :1@C2_:2@N6 7956 0.818 4.33 1.04 17 :1@N3_:2@C4 7922 0.814 5.3 0.705 18 :1@N3_:2@N3 7852 0.807 5.35 0.76 19 :1@N9_:2@C4 7813 0.803 5.6 0.848 20 :1@N3_:2@N7 7770 0.799 5.24 0.842 21 :1@N9_:2@N1 7768 0.798 5.24 0.956 22 :1@N9_:2@C8 7732 0.795 5.92 0.576 23 :1@C4_:2@N7 7724 0.794 5.45 0.689 24 :1@C5_:2@N6 7707 0.792 4.82 0.884 25 :1@C2_:2@C2 7653 0.787 5.03 0.943 26 :1@C4_:2@C2 7556 0.777 5.24 0.981 27 :1@N1_:2@N6 7547 0.776 4.51 0.954 28 :1@C5_:2@C6 7545 0.775 5.11 0.879 29 :1@C4_:2@C4 7523 0.773 5.59 0.734 30 :1@C2_:2@C5 7521 0.773 5.17 0.795 31 :1@C6_:2@N6 7443 0.765 4.75 0.905 32 :1@N1_:2@N1 7441 0.765 4.89 0.926 33 :1@N1_:2@C6 7395 0.76 4.95 0.826 34 :1@C8_:2@N6 7371 0.758 5.43 0.838 35 :1@C6_:2@C6 7193 0.739 5.2 0.834 36 :1@N7_:2@N6 7188 0.739 5.32 0.896 37 :1@C5_:2@N1 7182 0.738 5.11 1.05 38 :1@C8_:2@C6 7127 0.732 5.47 0.866 39 :1@N9_:2@C2 7081 0.728 5.38 1.06 40 :1@C5_:2@C5 7036 0.723 5.62 0.72 41 :1@C8_:2@N7 7029 0.722 5.94 0.729 42 :1@C6_:2@N1 7022 0.722 5.15 0.973 43 :1@C2_:2@C4 7017 0.721 5.64 0.662 44 :1@N9_:2@N9 7005 0.72 5.99 0.688 45 :1@N3_:2@N9 6998 0.719 5.88 0.582 46 :1@C8_:2@C5 6993 0.719 5.71 0.802 47 :1@C4_:2@N3 6973 0.717 5.6 0.838 48 :1@N3_:2@C8 6952 0.714 5.77 0.698 49 :1@C2_:2@N3 6923 0.712 5.6 0.754 50 :1@C4_:2@C8 6857 0.705 6.01 0.573 51 :1@N6_:2@N6 6805 0.699 5.25 0.876 52 :1@N9_:2@N3 6782 0.697 5.58 1.02 53 :1@C2_:2@N7 6718 0.69 5.56 0.81 54 :1@N7_:2@C6 6625 0.681 5.49 0.886 55 :1@N1_:2@C5 6610 0.679 5.67 0.66 56 :1@C5_:2@N7 6529 0.671 5.94 0.649 57 :1@C4_:2@N9 6351 0.653 6.11 0.558 58 :1@C6_:2@C5 6240 0.641 5.86 0.637 59 :1@C8_:2@N1 6172 0.634 5.39 1.04 60 :1@C5_:2@C2 6060 0.623 5.44 1.06 61 :1@N6_:2@C6 5927 0.609 5.73 0.753 62 :1@N7_:2@N1 5862 0.602 5.36 1.09 63 :1@N7_:2@C5 5775 0.594 5.84 0.774 64 :1@C6_:2@C2 5739 0.59 5.6 0.868 65 :1@N6_:2@N1 5645 0.58 5.56 0.887 66 :1@C5_:2@C4 5385 0.553 5.95 0.703 67 :1@N1_:2@N7 5373 0.552 6.03 0.683 68 :1@N1_:2@C4 5291 0.544 6.15 0.508 69 :1@N7_:2@N7 5272 0.542 6.11 0.756 70 :1@C2_:2@C8 5055 0.52 6.11 0.686 71 :1@C2_:2@N9 5016 0.516 6.23 0.541 72 :1@C8_:2@C2 4942 0.508 5.3 1.21 73 :1@C6_:2@N7 4939 0.508 6.14 0.591 74 :1@C8_:2@C4 4898 0.503 5.66 0.881 75 :1@C8_:2@C8 4860 0.499 6.19 0.666 76 :1@C5_:2@N3 4697 0.483 5.79 0.878 77 :1@N7_:2@C2 4296 0.442 5.3 1.21 78 :1@C8_:2@N3 4241 0.436 5.41 1.14 79 :1@C6_:2@C4 4226 0.434 6.22 0.519 80 :1@C8_:2@N9 3796 0.39 5.97 0.656 81 :1@C5_:2@C8 3778 0.388 6.33 0.479 82 :1@N7_:2@C4 3746 0.385 5.81 0.765 83 :1@N6_:2@C5 3613 0.371 6.25 0.543 84 :1@N7_:2@N3 3285 0.338 5.47 1.03 85 :1@C5_:2@N9 3084 0.317 6.36 0.46 86 :1@N7_:2@C8 2565 0.264 6.25 0.657 87 :1@N7_:2@N9 2471 0.254 6.24 0.591 88 :1@N1_:2@C8 2242 0.23 6.37 0.592 89 :1@N6_:2@N7 2090 0.215 6.35 0.493 90 :1@C6_:2@C8 1902 0.195 6.49 0.411 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0007 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 9730 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 9730 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 9730 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 9730 COM "COM" (double, distance), size is 9730 v_base1 "v_base1" (vector), size is 9730 v_base2 "v_base2" (vector), size is 9730 normalangle "normalangle" (double), size is 9730 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.7578 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.