CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 10:59:22 | Available memory: 5505.69 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.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.c0] Reading '../ctraj.c0' 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] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 178193 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 178193 of 178193) Coordinate processing will occur on 178193 frames. TIME: Run Initialization took 0.0014 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 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.c0 (1-178193, 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 86 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@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@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@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@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@N9' Atom ':1@N6' to ':2@C8' 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@N6' to ':2@C2' Atom ':1@N6' 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@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@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@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@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 178193 frames and processed 178193 frames. TIME: Trajectory processing: 1.0829 s TIME: Avg. throughput= 164556.8334 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 75.9239 86 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N7 176195 0.989 4.5 0.703 2 :1@N9_:2@C8 175737 0.986 4.78 0.786 3 :1@N9_:2@C5 175381 0.984 4.56 0.619 4 :1@N9_:2@N9 175376 0.984 5.09 0.591 5 :1@C4_:2@C5 174325 0.978 4.44 0.631 6 :1@C4_:2@N7 174109 0.977 4.52 0.798 7 :1@N9_:2@C4 173844 0.976 4.91 0.598 8 :1@C8_:2@N7 173749 0.975 4.59 0.876 9 :1@C8_:2@C5 173130 0.972 4.67 0.719 10 :1@C5_:2@C5 172595 0.969 4.51 0.762 11 :1@N9_:2@C6 172283 0.967 4.8 0.874 12 :1@C4_:2@C6 172181 0.966 4.5 0.739 13 :1@C4_:2@N6 172016 0.965 4.68 0.865 14 :1@C5_:2@N6 171905 0.965 4.21 0.75 15 :1@C4_:2@C4 171862 0.964 4.83 0.711 16 :1@C5_:2@N7 171750 0.964 4.66 0.947 17 :1@N7_:2@C5 171532 0.963 4.69 0.714 18 :1@C5_:2@C6 171184 0.961 4.3 0.69 19 :1@N7_:2@N6 171125 0.96 4.33 0.847 20 :1@C4_:2@C8 171083 0.96 4.9 0.983 21 :1@C8_:2@C6 170462 0.957 4.74 0.917 22 :1@N7_:2@C6 170402 0.956 4.5 0.771 23 :1@C8_:2@C8 170336 0.956 5.05 0.843 24 :1@N7_:2@N7 170298 0.956 4.72 0.939 25 :1@C8_:2@N9 170289 0.956 5.49 0.655 26 :1@C8_:2@C4 170211 0.955 5.19 0.693 27 :1@C4_:2@N9 170031 0.954 5.14 0.902 28 :1@N3_:2@C5 169916 0.954 4.69 0.727 29 :1@C8_:2@N6 169877 0.953 4.79 0.978 30 :1@N3_:2@N7 169325 0.95 4.83 0.861 31 :1@N9_:2@N6 169085 0.949 5.03 0.912 32 :1@C6_:2@N6 168809 0.947 4.19 0.797 33 :1@N3_:2@C6 167767 0.941 4.79 0.82 34 :1@C5_:2@C4 167343 0.939 5.09 0.832 35 :1@N7_:2@C4 166920 0.937 5.37 0.701 36 :1@C6_:2@C6 166779 0.936 4.38 0.82 37 :1@N6_:2@N6 166454 0.934 4.28 0.906 38 :1@C4_:2@N1 166433 0.934 4.86 0.94 39 :1@C5_:2@N1 165755 0.93 4.66 0.866 40 :1@N3_:2@C4 165388 0.928 4.86 0.849 41 :1@N3_:2@N6 164722 0.924 5.05 0.987 42 :1@C6_:2@C5 164673 0.924 4.78 0.98 43 :1@C4_:2@N3 163344 0.917 5.2 0.725 44 :1@N1_:2@N6 163322 0.917 4.56 0.898 45 :1@N7_:2@N1 163087 0.915 4.93 1.01 46 :1@N3_:2@C8 162570 0.912 5.01 1.06 47 :1@C6_:2@N7 161733 0.908 5.08 1.04 48 :1@C2_:2@C5 161713 0.908 4.87 0.866 49 :1@C2_:2@C6 161709 0.907 4.76 0.807 50 :1@N6_:2@C6 161070 0.904 4.66 0.992 51 :1@N1_:2@C6 160767 0.902 4.59 0.833 52 :1@C2_:2@N6 160749 0.902 4.9 0.991 53 :1@C5_:2@C8 160537 0.901 5.21 1.02 54 :1@N3_:2@N9 159986 0.898 5.08 1.09 55 :1@C6_:2@N1 159957 0.898 4.55 0.868 56 :1@C5_:2@C2 158153 0.888 5.14 0.843 57 :1@N1_:2@C5 157885 0.886 4.93 0.996 58 :1@N7_:2@C8 156672 0.879 5.29 0.87 59 :1@C2_:2@N7 156565 0.879 5.11 0.945 60 :1@N1_:2@N1 155421 0.872 4.64 0.93 61 :1@C5_:2@N3 155169 0.871 5.4 0.772 62 :1@C5_:2@N9 153753 0.863 5.49 0.93 63 :1@N7_:2@N9 152843 0.858 5.74 0.718 64 :1@N6_:2@N1 152177 0.854 4.72 0.987 65 :1@N1_:2@N7 151099 0.848 5.26 1 66 :1@C2_:2@C4 150772 0.846 4.99 1.09 67 :1@N7_:2@N3 150060 0.842 5.72 0.8 68 :1@N6_:2@C5 149651 0.84 5.2 1.06 69 :1@N7_:2@C2 149513 0.839 5.4 0.984 70 :1@C8_:2@N1 149060 0.837 5.01 1.06 71 :1@C8_:2@N3 147962 0.83 5.53 0.868 72 :1@C6_:2@C2 147759 0.829 5.02 0.932 73 :1@C6_:2@C4 145983 0.819 5.2 1.06 74 :1@N1_:2@C4 137715 0.773 5.1 1.19 75 :1@N6_:2@N7 136935 0.768 5.47 1.01 76 :1@C2_:2@C8 135006 0.758 5.23 1.08 77 :1@C6_:2@N3 132290 0.742 5.28 0.966 78 :1@C6_:2@C8 129197 0.725 5.46 1.06 79 :1@N6_:2@C2 129175 0.725 5.17 0.989 80 :1@C2_:2@N9 128913 0.723 5.16 1.23 81 :1@N1_:2@C8 114998 0.645 5.4 1.06 82 :1@N6_:2@C4 111508 0.626 5.44 1.02 83 :1@C6_:2@N9 110580 0.621 5.45 1.05 84 :1@N1_:2@N9 102539 0.575 5.24 1.17 85 :1@N6_:2@C8 84540 0.474 5.66 0.851 86 :1@N6_:2@N9 72034 0.404 5.61 0.784 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0100 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 178193 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 178193 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 178193 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 178193 COM "COM" (double, distance), size is 178193 v_base1 "v_base1" (vector), size is 178193 v_base2 "v_base2" (vector), size is 178193 normalangle "normalangle" (double), size is 178193 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: 1.4887 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.