CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:32:46 | Available memory: 6133.29 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.c1] Reading '../ctraj.c1' 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, 47427 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 47427 of 47427) Coordinate processing will occur on 47427 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.c1 (1-47427, 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 47427 frames and processed 47427 frames. TIME: Trajectory processing: 3.5875 s TIME: Avg. throughput= 13220.2208 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 76.6146 86 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N7 46530 0.981 4.81 0.773 2 :1@N3_:2@C5 46379 0.978 4.62 0.642 3 :1@N3_:2@C4 46181 0.974 4.66 0.655 4 :1@N3_:2@C8 45953 0.969 4.87 0.97 5 :1@C4_:2@C5 45919 0.968 4.51 0.598 6 :1@C4_:2@N7 45904 0.968 4.63 0.858 7 :1@N9_:2@N9 45897 0.968 5.12 0.673 8 :1@N9_:2@C8 45890 0.968 4.88 0.924 9 :1@N3_:2@N9 45882 0.967 4.82 0.96 10 :1@C4_:2@C4 45850 0.967 4.71 0.627 11 :1@C4_:2@N9 45754 0.965 4.92 0.913 12 :1@C2_:2@C5 45746 0.965 4.7 0.756 13 :1@N9_:2@C5 45738 0.964 4.89 0.599 14 :1@N9_:2@N7 45716 0.964 4.78 0.826 15 :1@N9_:2@C4 45679 0.963 5.08 0.56 16 :1@C4_:2@C8 45539 0.96 4.81 1.04 17 :1@C4_:2@C6 45522 0.96 4.73 0.671 18 :1@C2_:2@C4 45380 0.957 4.75 0.91 19 :1@N3_:2@C6 45296 0.955 4.81 0.876 20 :1@C4_:2@N3 45266 0.954 5.12 0.627 21 :1@C5_:2@C6 45017 0.949 4.5 0.737 22 :1@C2_:2@C6 45005 0.949 4.66 0.841 23 :1@N9_:2@C6 44993 0.949 5.28 0.736 24 :1@N1_:2@C6 44941 0.948 4.5 0.752 25 :1@C4_:2@N1 44882 0.946 5.07 0.855 26 :1@C2_:2@N7 44851 0.946 5.07 0.893 27 :1@C5_:2@C5 44842 0.945 4.52 0.877 28 :1@C4_:2@N6 44824 0.945 5.07 0.804 29 :1@C6_:2@C6 44755 0.944 4.36 0.789 30 :1@N1_:2@N1 44744 0.943 4.52 0.78 31 :1@N1_:2@C5 44696 0.942 4.76 0.902 32 :1@C5_:2@N1 44593 0.94 4.8 0.775 33 :1@C5_:2@C4 44567 0.94 4.89 0.893 34 :1@C5_:2@N6 44554 0.939 4.66 0.814 35 :1@C6_:2@N6 44503 0.938 4.45 0.853 36 :1@C6_:2@N1 44487 0.938 4.47 0.76 37 :1@C8_:2@C4 44092 0.93 5.45 0.763 38 :1@C6_:2@C5 44037 0.929 4.62 0.986 39 :1@N1_:2@N6 43922 0.926 4.64 0.936 40 :1@C5_:2@C2 43909 0.926 5.08 0.789 41 :1@C8_:2@C5 43819 0.924 5.06 0.851 42 :1@C5_:2@N3 43585 0.919 5.2 0.794 43 :1@N1_:2@C4 43509 0.917 4.89 1.12 44 :1@C6_:2@C2 43368 0.914 4.79 0.856 45 :1@C8_:2@C6 43201 0.911 5.31 0.851 46 :1@N9_:2@N6 42991 0.906 5.6 0.75 47 :1@N7_:2@C6 42931 0.905 4.85 0.918 48 :1@N6_:2@N6 42845 0.903 4.44 0.988 49 :1@N6_:2@C6 42768 0.902 4.53 1.01 50 :1@C6_:2@C4 42719 0.901 4.92 1.09 51 :1@N6_:2@N1 42611 0.898 4.51 0.951 52 :1@C5_:2@N7 42459 0.895 4.63 1.03 53 :1@C2_:2@N9 42449 0.895 5.01 1.16 54 :1@N3_:2@N6 42351 0.893 5.11 1.07 55 :1@N7_:2@C5 42199 0.89 4.81 0.953 56 :1@C2_:2@N6 42183 0.889 4.83 1.11 57 :1@N7_:2@N1 42182 0.889 5.25 0.935 58 :1@C2_:2@C8 42149 0.889 5.17 1.04 59 :1@C8_:2@N9 42064 0.887 5.52 0.778 60 :1@N7_:2@C4 41909 0.884 5.31 0.877 61 :1@N1_:2@N7 41804 0.881 5.19 0.97 62 :1@C6_:2@N3 41539 0.876 5.01 1 63 :1@N7_:2@N6 41315 0.871 4.82 0.937 64 :1@C5_:2@N9 40962 0.864 5.18 1.02 65 :1@C8_:2@N7 40889 0.862 4.76 0.998 66 :1@C8_:2@N6 40574 0.856 5.4 0.861 67 :1@C6_:2@N7 40443 0.853 4.92 1.01 68 :1@N6_:2@C2 39955 0.842 4.86 1.04 69 :1@N7_:2@N3 39497 0.833 5.65 0.866 70 :1@C8_:2@C8 39485 0.833 5.01 0.914 71 :1@N7_:2@C2 39413 0.831 5.51 0.945 72 :1@C5_:2@C8 39351 0.83 4.93 1.04 73 :1@N6_:2@C5 39247 0.828 4.91 1.05 74 :1@N7_:2@N7 38645 0.815 4.64 1.01 75 :1@C8_:2@N3 38089 0.803 5.77 0.819 76 :1@C8_:2@N1 37734 0.796 5.61 0.891 77 :1@N7_:2@N9 36809 0.776 5.49 0.85 78 :1@N7_:2@C8 36157 0.762 5.05 0.9 79 :1@N1_:2@C8 34935 0.737 5.27 0.998 80 :1@N6_:2@N7 34851 0.735 5.25 0.927 81 :1@C6_:2@C8 34835 0.734 5.17 0.992 82 :1@N1_:2@N9 34626 0.73 5.05 1.12 83 :1@N6_:2@C4 33769 0.712 5.08 1.03 84 :1@C6_:2@N9 33675 0.71 5.11 1.03 85 :1@N6_:2@C8 27093 0.571 5.52 0.747 86 :1@N6_:2@N9 25381 0.535 5.35 0.705 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0038 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 47427 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 47427 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 47427 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 47427 COM "COM" (double, distance), size is 47427 v_base1 "v_base1" (vector), size is 47427 v_base2 "v_base2" (vector), size is 47427 normalangle "normalangle" (double), size is 47427 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: 3.7116 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.