CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:37:14 | Available memory: 3726.61 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, 76662 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 76662 of 76662) Coordinate processing will occur on 76662 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 (1-76662, 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 76662 frames and processed 76662 frames. TIME: Trajectory processing: 5.9649 s TIME: Avg. throughput= 12852.1788 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 75.5593 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C5 74984 0.978 4.54 0.616 2 :1@N9_:2@N7 74939 0.978 4.76 0.81 3 :1@N9_:2@C5 74897 0.977 4.72 0.625 4 :1@N9_:2@C8 74791 0.976 5 0.883 5 :1@N3_:2@C5 74715 0.975 4.72 0.7 6 :1@N9_:2@N9 74677 0.974 5.19 0.65 7 :1@C4_:2@N7 74596 0.973 4.73 0.85 8 :1@N9_:2@C4 74576 0.973 4.98 0.582 9 :1@C4_:2@C4 74483 0.972 4.86 0.659 10 :1@C4_:2@C6 74423 0.971 4.57 0.698 11 :1@N9_:2@C6 73915 0.964 4.94 0.809 12 :1@C4_:2@N6 73758 0.962 4.78 0.843 13 :1@C5_:2@C6 73757 0.962 4.42 0.742 14 :1@N3_:2@C6 73637 0.961 4.76 0.859 15 :1@N3_:2@C4 73628 0.96 4.92 0.748 16 :1@C5_:2@C5 73571 0.96 4.64 0.837 17 :1@N3_:2@N7 73433 0.958 4.9 0.823 18 :1@C5_:2@N6 73410 0.958 4.41 0.837 19 :1@C4_:2@N9 73176 0.955 5.21 0.894 20 :1@C4_:2@N1 73142 0.954 4.87 0.894 21 :1@C6_:2@N6 73031 0.953 4.35 0.869 22 :1@C6_:2@C6 72918 0.951 4.49 0.821 23 :1@C4_:2@C8 72813 0.95 5.05 0.997 24 :1@C5_:2@N1 72476 0.945 4.67 0.835 25 :1@C8_:2@C5 72471 0.945 4.88 0.842 26 :1@C4_:2@N3 72362 0.944 5.19 0.677 27 :1@C5_:2@C4 72039 0.94 5.11 0.867 28 :1@C2_:2@C5 71974 0.939 4.91 0.802 29 :1@C2_:2@C6 71878 0.938 4.73 0.849 30 :1@N9_:2@N6 71847 0.937 5.22 0.85 31 :1@C8_:2@C4 71799 0.937 5.27 0.752 32 :1@N1_:2@C6 71616 0.934 4.65 0.795 33 :1@C8_:2@C6 71610 0.934 4.95 0.928 34 :1@N3_:2@N9 71315 0.93 5.19 0.993 35 :1@N1_:2@N6 71272 0.93 4.57 0.935 36 :1@C6_:2@N1 71266 0.93 4.58 0.837 37 :1@N7_:2@C6 71156 0.928 4.65 0.89 38 :1@N3_:2@C8 71150 0.928 5.12 0.979 39 :1@C6_:2@C5 71044 0.927 4.9 0.966 40 :1@N6_:2@N6 70840 0.924 4.47 0.971 41 :1@N3_:2@N6 70598 0.921 4.94 1.03 42 :1@N1_:2@N1 70521 0.92 4.69 0.88 43 :1@C5_:2@N7 70352 0.918 4.84 0.998 44 :1@N7_:2@C5 70298 0.917 4.82 0.88 45 :1@C5_:2@C2 70084 0.914 5.08 0.817 46 :1@N1_:2@C5 70017 0.913 5.03 0.908 47 :1@N7_:2@N6 69864 0.911 4.55 0.959 48 :1@N7_:2@N1 69382 0.905 4.95 0.98 49 :1@N6_:2@C6 69381 0.905 4.76 0.992 50 :1@C2_:2@N6 69295 0.904 4.75 1.07 51 :1@C8_:2@N9 69228 0.903 5.54 0.743 52 :1@C8_:2@N7 69213 0.903 4.81 0.986 53 :1@C2_:2@N7 69187 0.902 5.19 0.906 54 :1@C8_:2@N6 69115 0.902 5.03 0.966 55 :1@N7_:2@C4 68870 0.898 5.35 0.806 56 :1@C5_:2@N3 68844 0.898 5.34 0.788 57 :1@C2_:2@C4 68772 0.897 5.1 0.965 58 :1@N6_:2@N1 67623 0.882 4.75 0.977 59 :1@C6_:2@C2 67289 0.878 5.01 0.911 60 :1@C8_:2@C8 66327 0.865 5.16 0.915 61 :1@N7_:2@N7 65901 0.86 4.85 1.02 62 :1@C6_:2@N7 65429 0.853 5.18 0.987 63 :1@N7_:2@C2 65338 0.852 5.32 0.956 64 :1@C8_:2@N1 65137 0.85 5.17 1.02 65 :1@C6_:2@C4 64963 0.847 5.27 1.07 66 :1@N1_:2@N7 64961 0.847 5.38 0.948 67 :1@N7_:2@N3 64836 0.846 5.61 0.83 68 :1@C8_:2@N3 64775 0.845 5.53 0.849 69 :1@C5_:2@N9 63966 0.834 5.49 0.984 70 :1@N1_:2@C4 63697 0.831 5.26 1.12 71 :1@C5_:2@C8 63329 0.826 5.26 1.02 72 :1@N6_:2@C5 62008 0.809 5.24 1.03 73 :1@C6_:2@N3 61176 0.798 5.31 1 74 :1@C2_:2@C8 60813 0.793 5.4 1.02 75 :1@C2_:2@N9 59589 0.777 5.36 1.17 76 :1@N7_:2@N9 59574 0.777 5.68 0.815 77 :1@N6_:2@C2 59542 0.777 5.16 1.04 78 :1@N7_:2@C8 58871 0.768 5.3 0.91 79 :1@N6_:2@N7 53671 0.7 5.52 0.927 80 :1@C6_:2@C8 51538 0.672 5.5 1.01 81 :1@N1_:2@C8 48528 0.633 5.52 1.01 82 :1@N6_:2@C4 47619 0.621 5.43 1.06 83 :1@C6_:2@N9 46356 0.605 5.46 1.08 84 :1@N1_:2@N9 44294 0.578 5.35 1.17 85 :1@N6_:2@C8 33912 0.442 5.69 0.792 86 :1@N6_:2@N9 29057 0.379 5.5 0.778 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0059 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 76662 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 76662 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 76662 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 76662 COM "COM" (double, distance), size is 76662 v_base1 "v_base1" (vector), size is 76662 v_base2 "v_base2" (vector), size is 76662 normalangle "normalangle" (double), size is 76662 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: 6.1563 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.