CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 17:34:04 | Available memory: 49852.7 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@N1,C6,C5,C4,N4,N3,C2,O2', 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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [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] [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] [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', 63 atoms, 2 res, box: Orthogonal, 1 mol, 170542 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 170542 of 170542) Coordinate processing will occur on 170542 frames. TIME: Run Initialization took 0.0001 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*](39) Reference mask: [:1,2&!@H*](39) 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [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. 6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-170542, 1) ----- 0% Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 79 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C4' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@O2' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C4' Atom ':2@C8' to ':1@N4' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@O2' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C4' Atom ':2@N7' to ':1@N4' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@N4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@N4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C4' Atom ':2@N6' to ':1@N4' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@O2' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@N4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@N4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@N4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@N4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 170542 frames and processed 170542 frames. TIME: Trajectory processing: 0.9105 s TIME: Avg. throughput= 187303.8187 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 2 1 70.8667 79 # Contact Nframes Frac. Avg Stdev 1 :2@N7_:1@N1 168831 0.99 4.66 0.681 2 :2@N7_:1@C2 168512 0.988 4.75 0.845 3 :2@C5_:1@C2 168487 0.988 4.45 0.619 4 :2@C5_:1@O2 168327 0.987 4.6 0.771 5 :2@C8_:1@N1 168326 0.987 5.14 0.674 6 :2@C5_:1@N1 167614 0.983 4.49 0.575 7 :2@N9_:1@N1 167498 0.982 5.36 0.504 8 :2@C6_:1@O2 167115 0.98 4.45 0.781 9 :2@C4_:1@O2 166835 0.978 4.93 0.757 10 :2@N6_:1@O2 166665 0.977 4.66 0.868 11 :2@C4_:1@C2 166325 0.975 4.95 0.603 12 :2@N6_:1@C2 166263 0.975 4.26 0.711 13 :2@C6_:1@C2 166234 0.975 4.2 0.651 14 :2@C5_:1@N3 166150 0.974 4.74 0.718 15 :2@N9_:1@C2 166110 0.974 5.55 0.638 16 :2@N7_:1@N3 165207 0.969 5.09 0.921 17 :2@N6_:1@N3 165102 0.968 3.91 0.734 18 :2@C8_:1@C2 164817 0.966 5.34 0.82 19 :2@N7_:1@C6 164815 0.966 4.86 0.825 20 :2@C4_:1@N1 164783 0.966 4.9 0.541 21 :2@N7_:1@O2 164604 0.965 4.91 1.01 22 :2@C6_:1@N3 164234 0.963 4.18 0.683 23 :2@N9_:1@O2 163712 0.96 5.47 0.8 24 :2@C6_:1@N1 163222 0.957 4.43 0.663 25 :2@N6_:1@N1 162810 0.955 4.61 0.685 26 :2@N6_:1@C4 162558 0.953 3.92 0.727 27 :2@C5_:1@C6 161801 0.949 4.74 0.684 28 :2@C5_:1@C4 161728 0.948 4.99 0.649 29 :2@N7_:1@C4 161632 0.948 5.28 0.843 30 :2@C6_:1@C4 160845 0.943 4.38 0.675 31 :2@N6_:1@N4 160683 0.942 4.15 0.791 32 :2@N1_:1@C2 160662 0.942 4.41 0.816 33 :2@C4_:1@N3 160540 0.941 5.43 0.655 34 :2@N1_:1@O2 160039 0.938 4.51 0.908 35 :2@C8_:1@C6 159952 0.938 5.42 0.735 36 :2@N6_:1@C6 159301 0.934 4.57 0.85 37 :2@N1_:1@N3 159152 0.933 4.39 0.838 38 :2@N6_:1@C5 159148 0.933 4.24 0.863 39 :2@C6_:1@C6 159144 0.933 4.6 0.818 40 :2@N1_:1@N1 158848 0.931 4.75 0.877 41 :2@C5_:1@C5 158739 0.931 4.99 0.658 42 :2@N3_:1@C2 158394 0.929 5.17 0.702 43 :2@N7_:1@C5 158186 0.928 5.13 0.811 44 :2@N3_:1@O2 158075 0.927 5.03 0.875 45 :2@C4_:1@C6 157593 0.924 5.3 0.636 46 :2@C6_:1@C5 157499 0.924 4.57 0.782 47 :2@N3_:1@N1 157479 0.923 5.22 0.693 48 :2@C2_:1@C2 157215 0.922 4.83 0.854 49 :2@C6_:1@N4 157037 0.921 4.84 0.71 50 :2@N9_:1@C6 156673 0.919 5.77 0.57 51 :2@C8_:1@O2 155319 0.911 5.3 0.943 52 :2@N1_:1@C4 155054 0.909 4.66 0.849 53 :2@C2_:1@N1 154927 0.908 5.05 0.878 54 :2@C2_:1@O2 154000 0.903 4.71 0.955 55 :2@C4_:1@C4 152903 0.897 5.78 0.572 56 :2@C5_:1@N4 152828 0.896 5.61 0.673 57 :2@C2_:1@N3 152404 0.894 5.04 0.838 58 :2@C4_:1@C5 150647 0.883 5.72 0.593 59 :2@N1_:1@N4 149509 0.877 5.06 0.827 60 :2@N3_:1@N3 149451 0.876 5.59 0.692 61 :2@N1_:1@C6 149132 0.874 4.9 1.01 62 :2@N1_:1@C5 147765 0.866 4.87 0.974 63 :2@C2_:1@C4 144264 0.846 5.4 0.798 64 :2@C8_:1@N3 143068 0.839 5.73 0.79 65 :2@C8_:1@C5 141938 0.832 5.83 0.693 66 :2@N3_:1@C6 139475 0.818 5.54 0.757 67 :2@N9_:1@N3 139115 0.816 6.04 0.63 68 :2@N7_:1@N4 136685 0.801 5.78 0.772 69 :2@C2_:1@C6 134598 0.789 5.21 0.92 70 :2@N3_:1@C4 134168 0.787 5.96 0.605 71 :2@C8_:1@C4 130916 0.768 5.96 0.695 72 :2@C2_:1@C5 130286 0.764 5.4 0.874 73 :2@N9_:1@C5 128816 0.755 6.23 0.52 74 :2@N3_:1@C5 125386 0.735 5.89 0.677 75 :2@C2_:1@N4 123228 0.723 5.8 0.701 76 :2@N9_:1@C4 111755 0.655 6.28 0.507 77 :2@C4_:1@N4 108721 0.638 6.27 0.512 78 :2@N3_:1@N4 83321 0.489 6.31 0.497 79 :2@C8_:1@N4 70556 0.414 6.24 0.546 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0120 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 170542 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 170542 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 170542 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 170542 COM "COM" (double, distance), size is 170542 v_base2 "v_base2" (vector), size is 170542 v_base1 "v_base1" (vector), size is 170542 normalangle "normalangle" (double), size is 170542 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: 1.2542 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.