CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 10:59:32 | Available memory: 5404.02 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.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] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 165204 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 165204 of 165204) Coordinate processing will occur on 165204 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*](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 (1-165204, 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 52 native contacts: Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C5' to ':2@C6' 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@C6' 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@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' 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@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' 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 165204 frames and processed 165204 frames. TIME: Trajectory processing: 1.7325 s TIME: Avg. throughput= 95353.2574 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 47.2971 52 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 160740 0.973 4.87 0.667 2 :1@N3_:2@N9 158761 0.961 4.62 0.732 3 :1@C2_:2@N9 155781 0.943 4.67 0.788 4 :1@C4_:2@C4 155678 0.942 4.53 0.635 5 :1@C5_:2@C4 155222 0.94 4.58 0.727 6 :1@N3_:2@C8 154509 0.935 4.77 0.873 7 :1@N3_:2@C4 154411 0.935 4.48 0.643 8 :1@N9_:2@C4 153910 0.932 5.05 0.688 9 :1@N1_:2@N9 153870 0.931 5 0.726 10 :1@C6_:2@C4 153521 0.929 4.54 0.697 11 :1@C2_:2@C4 153508 0.929 4.41 0.757 12 :1@C4_:2@C5 153385 0.928 4.4 0.674 13 :1@C6_:2@N3 152987 0.926 4.37 0.732 14 :1@N1_:2@C4 152815 0.925 4.47 0.741 15 :1@N1_:2@N3 152773 0.925 4.26 0.727 16 :1@C5_:2@N3 152673 0.924 4.65 0.817 17 :1@C4_:2@N3 152658 0.924 4.79 0.768 18 :1@C2_:2@N3 152291 0.922 4.41 0.751 19 :1@N9_:2@C5 152181 0.921 4.7 0.757 20 :1@N3_:2@N3 152165 0.921 4.72 0.724 21 :1@C4_:2@N7 152159 0.921 4.61 0.89 22 :1@N3_:2@C5 152081 0.921 4.61 0.671 23 :1@C6_:2@C2 151236 0.915 4.16 0.76 24 :1@C4_:2@C6 151041 0.914 4.6 0.659 25 :1@C5_:2@C2 150707 0.912 4.49 0.882 26 :1@N3_:2@N7 150539 0.911 4.79 0.85 27 :1@N1_:2@C2 150347 0.91 4.27 0.749 28 :1@C2_:2@C5 150119 0.909 4.7 0.816 29 :1@C5_:2@C6 150065 0.908 4.23 0.75 30 :1@N3_:2@C6 149908 0.907 5.02 0.689 31 :1@N6_:2@N3 149891 0.907 4.67 0.763 32 :1@C5_:2@N1 149846 0.907 4.34 0.802 33 :1@C4_:2@N1 149705 0.906 4.87 0.769 34 :1@C6_:2@N1 149701 0.906 4.19 0.734 35 :1@C2_:2@C2 149699 0.906 4.68 0.81 36 :1@N6_:2@C2 149664 0.906 4.23 0.84 37 :1@C4_:2@C2 149579 0.905 4.89 0.859 38 :1@C2_:2@C8 149416 0.904 5.05 0.871 39 :1@N3_:2@C2 149105 0.903 5.04 0.828 40 :1@C6_:2@C6 148686 0.9 4.33 0.785 41 :1@N3_:2@N1 148364 0.898 5.24 0.796 42 :1@N1_:2@C5 148359 0.898 4.69 0.85 43 :1@N1_:2@N1 148106 0.897 4.53 0.802 44 :1@N9_:2@C6 147920 0.895 4.89 0.767 45 :1@C2_:2@N1 147184 0.891 4.99 0.857 46 :1@C2_:2@C6 146922 0.889 4.97 0.838 47 :1@N1_:2@C6 146698 0.888 4.7 0.868 48 :1@C2_:2@N7 145749 0.882 5.1 0.904 49 :1@N9_:2@N3 142714 0.864 5.4 0.844 50 :1@N3_:2@N6 142276 0.861 5.58 0.719 51 :1@N9_:2@C2 131724 0.797 5.35 0.89 52 :1@C2_:2@N6 130317 0.789 5.51 0.858 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0094 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 165204 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 165204 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 165204 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 165204 COM "COM" (double, distance), size is 165204 v_base1 "v_base1" (vector), size is 165204 v_base2 "v_base2" (vector), size is 165204 normalangle "normalangle" (double), size is 165204 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: 2.0608 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.