CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:24:06 | Available memory: 6.993 GB INPUT: Reading input from '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-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c2] Reading '../ctraj.c2' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*). Best-fit RMSD will be calculated, coords will be rotated and translated. [nativecontacts :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 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,N2,C2,N3,C4,C5,C6,O6,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_00002 Saving minimum observed distances in set 'Contacts_00002[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,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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 (1 total): 0: [traj] noWAt.topo.hmr, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 25153 of 25153) Coordinate processing will occur on 25153 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](42) Reference mask: [:1,2&!@H*](42) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c2 (1-25153, 1) ----- 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 72 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@N7' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C4' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@O6' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@O6' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 25153 frames and processed 25153 frames. TIME: Avg. throughput= 53430.0553 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 65.9523 72 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N9 25008 0.994 4.43 0.53 2 :2@N7_:1@N9 24927 0.991 4.74 0.748 3 :2@C4_:1@N9 24884 0.989 4.8 0.539 4 :2@C5_:1@C4 24868 0.989 4.66 0.675 5 :2@N9_:1@N9 24862 0.988 5.33 0.597 6 :2@C6_:1@N9 24798 0.986 4.33 0.567 7 :2@C6_:1@C4 24723 0.983 4.37 0.698 8 :2@C8_:1@N9 24714 0.983 5.22 0.755 9 :2@N6_:1@N9 24707 0.982 4.54 0.68 10 :2@C5_:1@C8 24695 0.982 4.62 0.666 11 :2@N6_:1@C4 24687 0.981 4.38 0.72 12 :2@C6_:1@C8 24641 0.98 4.34 0.679 13 :2@C4_:1@C4 24613 0.979 5.18 0.702 14 :2@N6_:1@C8 24571 0.977 4.38 0.859 15 :2@N7_:1@C4 24524 0.975 4.96 0.846 16 :2@N6_:1@C5 24515 0.975 4.16 0.764 17 :2@N6_:1@N7 24488 0.974 4.2 0.829 18 :2@C4_:1@C8 24459 0.972 5.07 0.651 19 :2@C6_:1@N7 24452 0.972 4.43 0.732 20 :2@C5_:1@N3 24449 0.972 5 0.803 21 :2@N3_:1@N9 24439 0.972 5.06 0.701 22 :2@C6_:1@C5 24438 0.972 4.41 0.782 23 :2@N1_:1@N9 24430 0.971 4.57 0.733 24 :2@C5_:1@C5 24337 0.968 4.95 0.797 25 :2@C5_:1@N7 24302 0.966 4.96 0.77 26 :2@C6_:1@N3 24269 0.965 4.79 0.875 27 :2@N7_:1@C8 24248 0.964 4.95 0.926 28 :2@N1_:1@C8 24242 0.964 4.52 0.826 29 :2@C2_:1@N9 24187 0.962 4.87 0.799 30 :2@N1_:1@C4 24151 0.96 4.6 0.88 31 :2@N6_:1@N3 24127 0.959 4.8 0.963 32 :2@N1_:1@C5 23889 0.95 4.59 0.966 33 :2@N1_:1@N7 23884 0.95 4.57 0.88 34 :2@C4_:1@N3 23763 0.945 5.46 0.737 35 :2@N6_:1@C6 23737 0.944 4.4 0.97 36 :2@C2_:1@C8 23672 0.941 4.9 0.898 37 :2@N3_:1@C8 23658 0.941 5.24 0.802 38 :2@N9_:1@C8 23385 0.93 5.65 0.696 39 :2@N3_:1@C4 23323 0.927 5.38 0.817 40 :2@C2_:1@C4 23322 0.927 5.02 0.935 41 :2@N9_:1@C4 23238 0.924 5.73 0.668 42 :2@N7_:1@C5 23182 0.922 5.26 0.916 43 :2@C6_:1@C6 23159 0.921 4.86 0.942 44 :2@N7_:1@N3 23148 0.92 5.12 0.937 45 :2@C8_:1@C4 23097 0.918 5.51 0.814 46 :2@C8_:1@C8 23089 0.918 5.5 0.86 47 :2@N7_:1@N7 23048 0.916 5.28 0.967 48 :2@C4_:1@N7 22797 0.906 5.5 0.718 49 :2@N6_:1@O6 22660 0.901 4.69 1.01 50 :2@N1_:1@N3 22596 0.898 4.91 0.961 51 :2@C4_:1@C5 22538 0.896 5.53 0.747 52 :2@C2_:1@N7 22507 0.895 5.1 0.956 53 :2@N6_:1@C2 22380 0.89 4.8 1.07 54 :2@N6_:1@N1 22335 0.888 4.64 1.03 55 :2@C6_:1@C2 22245 0.884 5.03 0.943 56 :2@C2_:1@C5 22109 0.879 5.14 0.97 57 :2@N1_:1@C6 21711 0.863 4.9 1.05 58 :2@C6_:1@N1 21498 0.855 5.04 0.929 59 :2@N9_:1@N3 21455 0.853 5.87 0.663 60 :2@C5_:1@C2 21422 0.852 5.37 0.813 61 :2@C5_:1@C6 21178 0.842 5.42 0.797 62 :2@C8_:1@N3 20973 0.834 5.56 0.842 63 :2@N3_:1@N7 20931 0.832 5.56 0.821 64 :2@C6_:1@O6 20719 0.824 5.21 0.892 65 :2@N3_:1@C5 20250 0.805 5.59 0.8 66 :2@N7_:1@C2 19376 0.77 5.38 0.906 67 :2@N7_:1@C6 19331 0.769 5.64 0.868 68 :2@N1_:1@O6 19123 0.76 5.17 0.972 69 :2@C8_:1@C5 18884 0.751 5.81 0.793 70 :2@N6_:1@N2 18447 0.733 5.15 1.07 71 :2@C8_:1@N7 18131 0.721 5.76 0.801 72 :2@N9_:1@N7 17953 0.714 6 0.644 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 25153, 'v_base2' size 25153, output size 25153 TIME: Analyses took 0.0039 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 25153 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 25153 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 25153 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 25153 COM "COM" (double, distance), size is 25153 v_base1 "v_base1" (vector, vector), size is 25153 v_base2 "v_base2" (vector, vector), size is 25153 normalangle "normalangle" (double), size is 25153 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.4708 s ( 99.09%) TIME: Action Post : 0.0003 s ( 0.06%) TIME: Analysis : 0.0039 s ( 0.82%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 0.4751 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.5889 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.