CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:34:06 | Available memory: 6126.73 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.c2] Reading '../ctraj.c2' 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, 34531 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 34531 of 34531) Coordinate processing will occur on 34531 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.c2 (1-34531, 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 75 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@N6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@N7' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@N6' Atom ':1@C8' to ':2@N1' Atom ':1@N7' to ':2@N7' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@N6' Atom ':1@N7' to ':2@N1' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@C8' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' 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@C8' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@N6' 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 34531 frames and processed 34531 frames. TIME: Trajectory processing: 2.5802 s TIME: Avg. throughput= 13382.9881 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 68.2044 75 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N9 34403 0.996 5.04 0.661 2 :1@N9_:2@C5 34400 0.996 4.29 0.544 3 :1@N9_:2@N7 34377 0.996 4.49 0.825 4 :1@N9_:2@C4 34295 0.993 4.62 0.532 5 :1@C4_:2@C5 34243 0.992 4.42 0.676 6 :1@C8_:2@C5 34186 0.99 4.37 0.673 7 :1@N9_:2@C8 34185 0.99 4.89 0.859 8 :1@N9_:2@C6 34150 0.989 4.36 0.544 9 :1@N9_:2@N6 34051 0.986 4.65 0.607 10 :1@C5_:2@C5 34024 0.985 4.6 0.759 11 :1@C4_:2@C4 34014 0.985 4.83 0.766 12 :1@C8_:2@C6 33992 0.984 4.24 0.633 13 :1@C4_:2@C6 33976 0.984 4.28 0.636 14 :1@C4_:2@N6 33945 0.983 4.44 0.703 15 :1@C8_:2@N6 33944 0.983 4.34 0.761 16 :1@N7_:2@C5 33944 0.983 4.6 0.752 17 :1@C5_:2@N6 33923 0.982 4.06 0.69 18 :1@N7_:2@N6 33896 0.982 4.02 0.755 19 :1@N7_:2@C6 33884 0.981 4.16 0.678 20 :1@C5_:2@C6 33881 0.981 4.15 0.677 21 :1@C4_:2@N7 33707 0.976 4.7 0.819 22 :1@C8_:2@N7 33705 0.976 4.6 0.961 23 :1@N9_:2@N3 33676 0.975 4.99 0.64 24 :1@N9_:2@N1 33603 0.973 4.68 0.742 25 :1@C8_:2@N1 33433 0.968 4.54 0.79 26 :1@N3_:2@C5 33344 0.966 4.81 0.772 27 :1@C5_:2@C4 33344 0.966 5.16 0.832 28 :1@C6_:2@N6 33274 0.964 4.29 0.858 29 :1@N9_:2@C2 33256 0.963 4.92 0.781 30 :1@C4_:2@N1 33245 0.963 4.51 0.791 31 :1@N7_:2@N1 33203 0.962 4.37 0.783 32 :1@N3_:2@C6 33189 0.961 4.75 0.801 33 :1@C4_:2@N9 33170 0.961 5.34 0.84 34 :1@C5_:2@N1 33166 0.96 4.31 0.809 35 :1@C6_:2@C6 33061 0.957 4.55 0.8 36 :1@C5_:2@N7 33051 0.957 4.97 0.845 37 :1@N7_:2@N7 32809 0.95 4.92 0.937 38 :1@N3_:2@N6 32781 0.949 4.94 0.944 39 :1@N6_:2@N6 32758 0.949 4.54 0.899 40 :1@C4_:2@C8 32641 0.945 5.18 0.857 41 :1@N3_:2@C4 32637 0.945 5.07 0.883 42 :1@C4_:2@N3 32576 0.943 5.05 0.797 43 :1@C4_:2@C2 32344 0.937 4.81 0.828 44 :1@C6_:2@C5 32122 0.93 5.13 0.772 45 :1@N3_:2@N7 32034 0.928 4.98 0.854 46 :1@C6_:2@N1 31883 0.923 4.53 0.908 47 :1@N6_:2@C6 31804 0.921 4.96 0.822 48 :1@N1_:2@N6 31738 0.919 4.72 0.986 49 :1@N3_:2@N1 31591 0.915 4.86 0.877 50 :1@C2_:2@C6 31472 0.911 4.93 0.816 51 :1@N1_:2@C6 31319 0.907 4.89 0.775 52 :1@C2_:2@N6 31098 0.901 4.92 1.04 53 :1@C2_:2@C5 31051 0.899 5.19 0.753 54 :1@N3_:2@N9 30974 0.897 5.45 0.967 55 :1@N3_:2@C8 30561 0.885 5.32 0.89 56 :1@N3_:2@N3 30560 0.885 5.18 0.963 57 :1@N1_:2@N1 30441 0.882 4.84 0.932 58 :1@N3_:2@C2 30303 0.878 5.01 0.942 59 :1@C2_:2@N1 30297 0.877 4.94 0.935 60 :1@C6_:2@N7 30293 0.877 5.52 0.757 61 :1@N1_:2@C5 30215 0.875 5.37 0.715 62 :1@C5_:2@C8 29853 0.865 5.56 0.777 63 :1@C2_:2@N7 29218 0.846 5.42 0.835 64 :1@C2_:2@C4 28608 0.828 5.43 0.921 65 :1@N1_:2@N7 28119 0.814 5.72 0.759 66 :1@C2_:2@C2 27368 0.793 5.05 1.03 67 :1@N1_:2@C2 26979 0.781 5.11 1.08 68 :1@N1_:2@C4 25701 0.744 5.64 0.876 69 :1@C2_:2@N3 25464 0.737 5.29 1.09 70 :1@C2_:2@C8 24260 0.703 5.71 0.759 71 :1@N6_:2@N7 24241 0.702 6 0.662 72 :1@C2_:2@N9 22978 0.665 5.75 0.943 73 :1@C6_:2@C8 22948 0.665 6.02 0.66 74 :1@N1_:2@C8 19649 0.569 6.05 0.652 75 :1@N1_:2@N9 16337 0.473 5.91 0.784 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0028 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 34531 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 34531 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 34531 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 34531 COM "COM" (double, distance), size is 34531 v_base1 "v_base1" (vector), size is 34531 v_base2 "v_base2" (vector), size is 34531 normalangle "normalangle" (double), size is 34531 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: 2.6775 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.