CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:34:17 | Available memory: 8372.84 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, 49913 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 49913 of 49913) Coordinate processing will occur on 49913 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 (1-49913, 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 75 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@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@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@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@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@N6' to ':2@N7' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' 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@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@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 49913 frames and processed 49913 frames. TIME: Trajectory processing: 4.2240 s TIME: Avg. throughput= 11816.5890 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 66.7043 75 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 49641 0.995 4.7 0.661 2 :1@C4_:2@C5 49456 0.991 4.68 0.646 3 :1@N9_:2@C6 49250 0.987 4.66 0.705 4 :1@N9_:2@C4 49227 0.986 4.97 0.616 5 :1@N9_:2@N7 49218 0.986 4.98 0.835 6 :1@C4_:2@C6 49202 0.986 4.4 0.671 7 :1@C4_:2@N6 49180 0.985 4.46 0.731 8 :1@C4_:2@C4 48819 0.978 5.15 0.621 9 :1@N9_:2@N6 48794 0.978 4.92 0.766 10 :1@N9_:2@N9 48784 0.977 5.44 0.618 11 :1@C5_:2@C6 48746 0.977 4.54 0.841 12 :1@C5_:2@N6 48611 0.974 4.36 0.914 13 :1@N9_:2@C8 48581 0.973 5.37 0.796 14 :1@C4_:2@N7 48563 0.973 5.02 0.805 15 :1@N3_:2@C5 48376 0.969 4.75 0.72 16 :1@C5_:2@C5 48327 0.968 5.03 0.798 17 :1@N3_:2@C6 48275 0.967 4.47 0.799 18 :1@C4_:2@N1 48237 0.966 4.58 0.825 19 :1@N9_:2@N1 48062 0.963 4.86 0.812 20 :1@N3_:2@N6 48061 0.963 4.48 0.866 21 :1@C6_:2@N6 48014 0.962 4.36 0.932 22 :1@C6_:2@C6 47625 0.954 4.78 0.84 23 :1@C8_:2@C5 47458 0.951 4.97 0.927 24 :1@N3_:2@C4 47386 0.949 5.22 0.666 25 :1@N9_:2@N3 47326 0.948 5.16 0.7 26 :1@C5_:2@N1 47245 0.947 4.63 0.914 27 :1@C8_:2@C6 47075 0.943 4.81 0.961 28 :1@N1_:2@N6 46939 0.94 4.37 0.89 29 :1@N9_:2@C2 46921 0.94 5.03 0.823 30 :1@N3_:2@N7 46908 0.94 5.02 0.836 31 :1@C4_:2@N9 46865 0.939 5.73 0.601 32 :1@C2_:2@N6 46700 0.936 4.34 0.958 33 :1@C4_:2@C2 46698 0.936 4.96 0.845 34 :1@C4_:2@N3 46546 0.933 5.3 0.708 35 :1@C2_:2@C6 46502 0.932 4.58 0.841 36 :1@N3_:2@N1 46473 0.931 4.6 0.901 37 :1@C4_:2@C8 46417 0.93 5.57 0.754 38 :1@N1_:2@C6 46212 0.926 4.8 0.767 39 :1@N7_:2@C6 46121 0.924 4.74 0.968 40 :1@C5_:2@C4 45931 0.92 5.56 0.689 41 :1@C6_:2@N1 45860 0.919 4.81 0.905 42 :1@C2_:2@C5 45857 0.919 5.1 0.742 43 :1@N6_:2@N6 45716 0.916 4.72 1.01 44 :1@N7_:2@N6 45369 0.909 4.59 1.07 45 :1@C6_:2@C5 45331 0.908 5.43 0.746 46 :1@C8_:2@N6 45275 0.907 4.87 1.02 47 :1@C8_:2@N1 45233 0.906 4.9 0.976 48 :1@C2_:2@N1 45113 0.904 4.68 0.976 49 :1@N1_:2@N1 45070 0.903 4.86 0.902 50 :1@N3_:2@N9 45017 0.902 5.79 0.621 51 :1@N3_:2@N3 44922 0.9 5.36 0.787 52 :1@N7_:2@C5 44852 0.899 5.12 0.888 53 :1@C5_:2@N7 44819 0.898 5.33 0.872 54 :1@N3_:2@C2 44767 0.897 4.98 0.929 55 :1@N3_:2@C8 44525 0.892 5.57 0.776 56 :1@N7_:2@N1 44509 0.892 4.79 0.986 57 :1@N1_:2@C5 44313 0.888 5.48 0.685 58 :1@C8_:2@N7 44122 0.884 5.14 1.04 59 :1@N6_:2@C6 43746 0.876 5.27 0.863 60 :1@C2_:2@N7 43166 0.865 5.37 0.866 61 :1@C2_:2@C4 42667 0.855 5.67 0.638 62 :1@C2_:2@C2 41376 0.829 5.17 0.947 63 :1@N7_:2@N7 40411 0.81 5.31 0.973 64 :1@N1_:2@C2 40009 0.802 5.46 0.866 65 :1@C6_:2@N7 39600 0.793 5.68 0.782 66 :1@N1_:2@N7 39441 0.79 5.74 0.802 67 :1@C2_:2@N3 38587 0.773 5.69 0.75 68 :1@N1_:2@C4 37466 0.751 6.05 0.547 69 :1@C5_:2@C8 36999 0.741 5.87 0.724 70 :1@C2_:2@C8 34869 0.699 5.94 0.739 71 :1@C2_:2@N9 33264 0.666 6.21 0.567 72 :1@N6_:2@N7 27890 0.559 6.05 0.681 73 :1@C6_:2@C8 25570 0.512 6.2 0.643 74 :1@N1_:2@C8 23007 0.461 6.19 0.668 75 :1@N1_:2@N9 17902 0.359 6.44 0.508 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0043 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 49913 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 49913 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 49913 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 49913 COM "COM" (double, distance), size is 49913 v_base1 "v_base1" (vector), size is 49913 v_base2 "v_base2" (vector), size is 49913 normalangle "normalangle" (double), size is 49913 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: 4.3739 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.