CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 13:32:01 | Available memory: 48628.8 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,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2' Mask2=':2@N1,C6,C5,C4,O4,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 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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', 59 atoms, 2 res, box: Orthogonal, 1 mol, 118569 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 118569 of 118569) Coordinate processing will occur on 118569 frames. TIME: Run Initialization took 0.0005 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*](37) Reference mask: [:1,2&!@H*](37) 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,C6,C5,C4,O4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 7 atoms. ----- ctraj.c1 (1-118569, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 64 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@O4' to ':2@N1' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@C5' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' Atom ':1@O4' to ':2@N3' Atom ':1@O4' to ':2@C2' Atom ':1@O4' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 118569 frames and processed 118569 frames. TIME: Trajectory processing: 0.5669 s TIME: Avg. throughput= 209136.6887 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 61.8513 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 118277 0.998 4.29 0.495 2 :1@C6_:2@C6 118251 0.997 4.15 0.547 3 :1@N1_:2@N1 118216 0.997 4.6 0.446 4 :1@C6_:2@N1 118051 0.996 4.64 0.568 5 :1@C6_:2@C5 118008 0.995 3.98 0.571 6 :1@N1_:2@C5 117969 0.995 4.48 0.546 7 :1@C2_:2@N1 117788 0.993 4.47 0.679 8 :1@C4_:2@C2 117748 0.993 4.19 0.685 9 :1@C5_:2@C6 117725 0.993 4.27 0.627 10 :1@C5_:2@N1 117723 0.993 4.58 0.689 11 :1@C4_:2@N3 117602 0.992 3.95 0.652 12 :1@C2_:2@C6 117547 0.991 4.52 0.707 13 :1@N1_:2@C2 117539 0.991 5.05 0.514 14 :1@C5_:2@C5 117523 0.991 3.87 0.637 15 :1@C5_:2@N3 117506 0.991 4.14 0.643 16 :1@C4_:2@N1 117502 0.991 4.49 0.673 17 :1@C5_:2@C2 117498 0.991 4.51 0.718 18 :1@C6_:2@C4 117441 0.99 4.34 0.559 19 :1@N1_:2@C4 117433 0.99 4.98 0.55 20 :1@C6_:2@C2 117396 0.99 4.93 0.613 21 :1@C5_:2@C4 117366 0.99 3.82 0.602 22 :1@C6_:2@N3 117324 0.989 4.76 0.597 23 :1@N3_:2@N1 117305 0.989 4.39 0.722 24 :1@C4_:2@C4 117181 0.988 4.02 0.7 25 :1@N1_:2@N3 117168 0.988 5.19 0.556 26 :1@N3_:2@C2 117134 0.988 4.27 0.736 27 :1@O4_:2@N3 117105 0.988 3.92 0.748 28 :1@C4_:2@C6 117071 0.987 4.55 0.648 29 :1@C4_:2@C5 116995 0.987 4.32 0.711 30 :1@O4_:2@C2 116761 0.985 4.32 0.787 31 :1@C2_:2@C2 116707 0.984 4.72 0.69 32 :1@N3_:2@C6 116550 0.983 4.59 0.719 33 :1@N3_:2@N3 116537 0.983 4.37 0.769 34 :1@C2_:2@C5 116405 0.982 4.82 0.728 35 :1@C4_:2@O2 116355 0.981 4.6 0.787 36 :1@O4_:2@C4 116172 0.98 4.15 0.78 37 :1@C5_:2@O4 116123 0.979 4.05 0.657 38 :1@C6_:2@O4 116111 0.979 4.75 0.62 39 :1@N3_:2@C5 115680 0.976 4.68 0.768 40 :1@N3_:2@O2 115571 0.975 4.55 0.768 41 :1@C2_:2@N3 115511 0.974 4.99 0.716 42 :1@C4_:2@O4 115510 0.974 4.32 0.784 43 :1@N3_:2@C4 115479 0.974 4.6 0.785 44 :1@O4_:2@N1 115309 0.973 4.92 0.724 45 :1@O4_:2@O2 115201 0.972 4.54 0.912 46 :1@C2_:2@C4 114801 0.968 5.08 0.713 47 :1@O4_:2@C5 114581 0.966 4.77 0.727 48 :1@O4_:2@C6 114417 0.965 5.12 0.655 49 :1@C5_:2@O2 114356 0.964 5.16 0.821 50 :1@O4_:2@O4 114252 0.964 4.25 0.88 51 :1@N1_:2@O4 114214 0.963 5.57 0.588 52 :1@C2_:2@O2 114129 0.963 5.11 0.705 53 :1@N1_:2@O2 113764 0.959 5.67 0.572 54 :1@O2_:2@N1 113369 0.956 4.81 0.81 55 :1@O2_:2@C6 113069 0.954 5.03 0.808 56 :1@C6_:2@O2 111760 0.943 5.64 0.68 57 :1@N3_:2@O4 111336 0.939 5.09 0.804 58 :1@O2_:2@C2 110614 0.933 5.11 0.824 59 :1@O2_:2@C5 107982 0.911 5.48 0.807 60 :1@C2_:2@O4 106788 0.901 5.66 0.684 61 :1@O2_:2@O2 106582 0.899 5.32 0.829 62 :1@O2_:2@N3 104318 0.88 5.54 0.796 63 :1@O2_:2@C4 100077 0.844 5.73 0.775 64 :1@O2_:2@O4 67863 0.572 6.12 0.711 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0061 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 118569 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 118569 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 118569 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 118569 COM "COM" (double, distance), size is 118569 v_base1 "v_base1" (vector), size is 118569 v_base2 "v_base2" (vector), size is 118569 normalangle "normalangle" (double), size is 118569 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: 0.7833 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.