CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:37:38 | Available memory: 6081.13 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.c5] Reading '../ctraj.c5' 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, 14198 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 14198 of 14198) Coordinate processing will occur on 14198 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.c5 (1-14198, 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 14198 frames and processed 14198 frames. TIME: Trajectory processing: 1.0665 s TIME: Avg. throughput= 13312.9922 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 40.2933 52 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 13215 0.931 5.17 0.841 2 :1@C2_:2@N9 12877 0.907 4.89 0.979 3 :1@C2_:2@C4 12547 0.884 4.56 1.04 4 :1@N3_:2@C4 12470 0.878 4.86 0.857 5 :1@C2_:2@N3 12422 0.875 4.53 0.996 6 :1@N3_:2@N3 12142 0.855 4.74 1.02 7 :1@N1_:2@N9 12034 0.848 5.12 0.901 8 :1@N1_:2@N3 11922 0.84 4.6 0.893 9 :1@C4_:2@N9 11865 0.836 5.51 0.669 10 :1@N1_:2@C4 11680 0.823 4.57 0.94 11 :1@C4_:2@C4 11625 0.819 5.13 0.766 12 :1@N3_:2@C8 11561 0.814 5.26 0.998 13 :1@C2_:2@C2 11559 0.814 4.53 0.906 14 :1@C4_:2@N3 11435 0.805 4.96 1.07 15 :1@C2_:2@C8 11423 0.805 5.01 1.03 16 :1@N3_:2@C5 11406 0.803 4.95 0.802 17 :1@N1_:2@C2 11389 0.802 4.45 0.865 18 :1@C2_:2@C5 11337 0.798 4.51 0.967 19 :1@C6_:2@N3 11301 0.796 4.87 0.83 20 :1@N3_:2@C2 11280 0.794 4.79 1.04 21 :1@C6_:2@C4 11085 0.781 4.9 0.832 22 :1@C6_:2@C2 11080 0.78 4.66 0.879 23 :1@C2_:2@N1 11037 0.777 4.63 0.808 24 :1@C2_:2@C6 10996 0.774 4.61 0.855 25 :1@C4_:2@C5 10992 0.774 5.21 0.734 26 :1@N3_:2@C6 10969 0.773 5.11 0.704 27 :1@N1_:2@N1 10959 0.772 4.39 0.842 28 :1@N1_:2@C5 10904 0.768 4.41 0.959 29 :1@C5_:2@N3 10894 0.767 5.03 0.992 30 :1@C5_:2@C4 10861 0.765 5.16 0.823 31 :1@N3_:2@N1 10824 0.762 5.05 0.809 32 :1@N1_:2@C6 10818 0.762 4.36 0.932 33 :1@C6_:2@N1 10724 0.755 4.55 0.892 34 :1@C4_:2@C2 10722 0.755 4.86 1.18 35 :1@C5_:2@C2 10672 0.752 4.86 1.12 36 :1@C4_:2@C6 10653 0.75 5.26 0.738 37 :1@C2_:2@N7 10642 0.75 4.82 1.02 38 :1@N6_:2@N3 10600 0.747 5.29 0.788 39 :1@N6_:2@C2 10592 0.746 4.97 0.831 40 :1@C6_:2@C6 10582 0.745 4.57 0.971 41 :1@C4_:2@N1 10529 0.742 5.11 0.963 42 :1@N9_:2@C4 10494 0.739 5.72 0.71 43 :1@N3_:2@N7 10406 0.733 5.13 0.986 44 :1@C5_:2@N1 10403 0.733 4.89 1.04 45 :1@C5_:2@C6 10313 0.726 5.01 0.902 46 :1@C2_:2@N6 10197 0.718 5.07 0.863 47 :1@N9_:2@C5 9956 0.701 5.87 0.59 48 :1@N3_:2@N6 9863 0.695 5.59 0.698 49 :1@C4_:2@N7 9777 0.689 5.4 0.863 50 :1@N9_:2@C6 9258 0.652 5.88 0.658 51 :1@N9_:2@N3 8910 0.628 5.14 1.02 52 :1@N9_:2@C2 7882 0.555 4.82 1.07 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0011 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 14198 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 14198 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 14198 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 14198 COM "COM" (double, distance), size is 14198 v_base1 "v_base1" (vector), size is 14198 v_base2 "v_base2" (vector), size is 14198 normalangle "normalangle" (double), size is 14198 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: 1.1176 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.