CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:13:52 | Available memory: 1.231 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 23764 of 23764) Coordinate processing will occur on 23764 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 (1-23764, 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 90 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@N2' 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@C2' Atom ':2@C8' to ':1@N2' 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@N1' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N2' 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@N1' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N2' 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@N2' 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@N1' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@N2' 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@C6' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@N2' Atom ':2@C2' to ':1@N3' 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@C2' Atom ':2@N3' to ':1@N3' 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@C2' Atom ':2@C4' to ':1@N2' 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 23764 frames and processed 23764 frames. TIME: Avg. throughput= 55540.7534 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 80.4904 90 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N9 23637 0.995 4.56 0.602 2 :2@C5_:1@C4 23610 0.994 4.59 0.617 3 :2@C4_:1@N9 23514 0.989 4.82 0.557 4 :2@N7_:1@N9 23473 0.988 4.86 0.803 5 :2@C6_:1@C4 23469 0.988 4.36 0.662 6 :2@N9_:1@N9 23442 0.986 5.31 0.583 7 :2@C4_:1@C4 23439 0.986 5.05 0.651 8 :2@N6_:1@C4 23432 0.986 4.45 0.708 9 :2@C6_:1@N9 23431 0.986 4.53 0.661 10 :2@C5_:1@N3 23340 0.982 4.8 0.73 11 :2@C8_:1@N9 23279 0.98 5.25 0.775 12 :2@N7_:1@C4 23256 0.979 4.88 0.823 13 :2@C6_:1@C5 23235 0.978 4.38 0.771 14 :2@N6_:1@N9 23169 0.975 4.81 0.746 15 :2@C5_:1@C5 23159 0.975 4.87 0.759 16 :2@N6_:1@C5 23130 0.973 4.22 0.795 17 :2@C6_:1@N3 23122 0.973 4.63 0.824 18 :2@N6_:1@N3 23018 0.969 4.68 0.914 19 :2@N1_:1@N9 22973 0.967 4.72 0.782 20 :2@N3_:1@N9 22962 0.966 5.04 0.704 21 :2@C5_:1@C8 22941 0.965 4.77 0.806 22 :2@N1_:1@C4 22930 0.965 4.57 0.883 23 :2@C4_:1@N3 22896 0.963 5.26 0.712 24 :2@N6_:1@C6 22881 0.963 4.32 0.888 25 :2@C6_:1@C8 22858 0.962 4.56 0.861 26 :2@N9_:1@C4 22835 0.961 5.62 0.659 27 :2@C6_:1@C6 22714 0.956 4.72 0.885 28 :2@C4_:1@C8 22714 0.956 5.09 0.665 29 :2@C2_:1@N9 22713 0.956 4.91 0.826 30 :2@N1_:1@C5 22701 0.955 4.5 0.944 31 :2@C6_:1@N7 22654 0.953 4.5 0.844 32 :2@N7_:1@N3 22503 0.947 4.93 0.871 33 :2@N6_:1@N7 22452 0.945 4.38 1.01 34 :2@N6_:1@N1 22434 0.944 4.49 0.957 35 :2@N1_:1@C8 22426 0.944 4.65 0.901 36 :2@C8_:1@C4 22425 0.944 5.42 0.815 37 :2@C4_:1@C5 22326 0.939 5.42 0.718 38 :2@N3_:1@C4 22320 0.939 5.24 0.796 39 :2@N6_:1@C8 22318 0.939 4.67 0.995 40 :2@C5_:1@N7 22290 0.938 4.94 0.794 41 :2@N1_:1@N7 22199 0.934 4.56 0.898 42 :2@N6_:1@O6 22195 0.934 4.62 0.985 43 :2@N6_:1@C2 22179 0.933 4.58 1.02 44 :2@C2_:1@C4 22166 0.933 4.92 0.935 45 :2@N3_:1@C8 22094 0.93 5.18 0.769 46 :2@N7_:1@C5 22056 0.928 5.19 0.915 47 :2@C5_:1@C2 22054 0.928 5.17 0.797 48 :2@C6_:1@C2 22032 0.927 4.78 0.891 49 :2@C2_:1@C8 22030 0.927 4.9 0.897 50 :2@C6_:1@N1 21964 0.924 4.86 0.886 51 :2@N7_:1@C8 21964 0.924 5.08 0.997 52 :2@N9_:1@N3 21925 0.923 5.73 0.689 53 :2@C5_:1@C6 21849 0.919 5.35 0.814 54 :2@N9_:1@C8 21791 0.917 5.64 0.662 55 :2@C4_:1@N7 21659 0.911 5.43 0.672 56 :2@N1_:1@N3 21519 0.906 4.77 0.943 57 :2@C8_:1@N3 21519 0.906 5.43 0.851 58 :2@N1_:1@C6 21407 0.901 4.71 1.01 59 :2@C2_:1@C5 21332 0.898 4.98 0.934 60 :2@C2_:1@N7 21325 0.897 4.99 0.911 61 :2@C5_:1@N1 21311 0.897 5.44 0.8 62 :2@C6_:1@O6 21111 0.888 5.13 0.892 63 :2@N7_:1@C2 20802 0.875 5.26 0.926 64 :2@N3_:1@N7 20796 0.875 5.48 0.782 65 :2@C8_:1@C8 20793 0.875 5.53 0.866 66 :2@N3_:1@N3 20712 0.872 5.4 0.858 67 :2@N7_:1@N7 20690 0.871 5.26 0.983 68 :2@N1_:1@N1 20492 0.862 4.87 1.04 69 :2@N3_:1@C5 20482 0.862 5.46 0.764 70 :2@N1_:1@C2 20415 0.859 4.85 1.02 71 :2@C2_:1@N3 20299 0.854 5.06 1 72 :2@C4_:1@C2 19824 0.834 5.67 0.706 73 :2@N1_:1@O6 19698 0.829 5.02 0.947 74 :2@N7_:1@C6 19671 0.828 5.58 0.904 75 :2@N6_:1@N2 19525 0.822 4.87 1.15 76 :2@C6_:1@N2 19454 0.819 5.16 0.931 77 :2@N7_:1@N1 19397 0.816 5.59 0.915 78 :2@C5_:1@N2 19043 0.801 5.51 0.818 79 :2@C2_:1@C6 18730 0.788 5.24 0.905 80 :2@C2_:1@C2 17851 0.751 5.18 1.02 81 :2@N7_:1@N2 17548 0.738 5.4 0.916 82 :2@C8_:1@C2 17297 0.728 5.77 0.871 83 :2@C2_:1@N1 17182 0.723 5.3 0.946 84 :2@N1_:1@N2 17089 0.719 5.11 0.953 85 :2@N3_:1@C2 16719 0.704 5.64 0.812 86 :2@N9_:1@C2 15859 0.667 6.11 0.689 87 :2@C4_:1@N2 15817 0.666 5.96 0.672 88 :2@C2_:1@N2 14612 0.615 5.38 1.01 89 :2@C8_:1@N2 13685 0.576 5.85 0.847 90 :2@N9_:1@N2 10191 0.429 6.16 0.675 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 23764, 'v_base2' size 23764, output size 23764 TIME: Analyses took 0.0030 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 23764 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 23764 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 23764 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 23764 COM "COM" (double, distance), size is 23764 v_base1 "v_base1" (vector, vector), size is 23764 v_base2 "v_base2" (vector, vector), size is 23764 normalangle "normalangle" (double), size is 23764 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.4279 s ( 99.21%) TIME: Action Post : 0.0003 s ( 0.06%) TIME: Analysis : 0.0030 s ( 0.70%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4313 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: 0.5894 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.