CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:23:58 | Available memory: 7.084 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.c0] Reading '../ctraj.c0' 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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 35021 of 35021) Coordinate processing will occur on 35021 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.c0 (1-35021, 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 108 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@C5' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@O6' Atom ':2@N9' to ':1@N1' 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@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@O6' Atom ':2@C8' to ':1@N1' 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@O6' 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@O6' 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@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@O6' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C2' 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@C6' Atom ':2@N3' to ':1@O6' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@N2' 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@C6' Atom ':2@C4' to ':1@O6' Atom ':2@C4' to ':1@N1' 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 35021 frames and processed 35021 frames. TIME: Avg. throughput= 51111.2214 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 99.9878 108 # Contact Nframes Frac. Avg Stdev 1 :2@N9_:1@N3 34695 0.991 4.56 0.606 2 :2@N9_:1@C4 34595 0.988 4.66 0.596 3 :2@C4_:1@N3 34585 0.988 4.41 0.596 4 :2@C4_:1@C4 34490 0.985 4.31 0.555 5 :2@N9_:1@C2 34445 0.984 4.84 0.64 6 :2@C4_:1@C2 34410 0.983 4.55 0.71 7 :2@N9_:1@N9 34386 0.982 4.93 0.691 8 :2@N3_:1@N3 34356 0.981 4.56 0.641 9 :2@C4_:1@N9 34286 0.979 4.68 0.635 10 :2@C5_:1@C4 34280 0.979 4.31 0.666 11 :2@C5_:1@N3 34272 0.979 4.69 0.707 12 :2@N3_:1@C4 34237 0.978 4.5 0.634 13 :2@N3_:1@C2 34224 0.977 4.39 0.705 14 :2@C4_:1@C5 34219 0.977 4.42 0.636 15 :2@C4_:1@N1 34145 0.975 4.66 0.683 16 :2@N9_:1@C5 34144 0.975 5.07 0.637 17 :2@C5_:1@N9 34129 0.975 4.42 0.691 18 :2@C8_:1@C4 34110 0.974 4.82 0.771 19 :2@C8_:1@N3 34083 0.973 4.88 0.736 20 :2@C4_:1@C6 34065 0.973 4.64 0.638 21 :2@N3_:1@N1 34058 0.973 4.26 0.66 22 :2@N3_:1@C5 34047 0.972 4.39 0.705 23 :2@N3_:1@C6 34030 0.972 4.29 0.666 24 :2@N9_:1@N1 34025 0.972 5.23 0.583 25 :2@C5_:1@C5 34003 0.971 4.34 0.764 26 :2@C6_:1@C4 33969 0.97 4.52 0.652 27 :2@C2_:1@N3 33949 0.969 4.93 0.709 28 :2@C2_:1@C4 33880 0.967 4.64 0.666 29 :2@N1_:1@C4 33863 0.967 4.71 0.628 30 :2@C2_:1@C5 33839 0.966 4.23 0.703 31 :2@C2_:1@C6 33827 0.966 4.04 0.713 32 :2@N7_:1@C4 33795 0.965 4.64 0.837 33 :2@N1_:1@C5 33784 0.965 4.18 0.691 34 :2@C2_:1@C2 33782 0.965 4.68 0.803 35 :2@C6_:1@N9 33775 0.964 4.66 0.647 36 :2@N9_:1@C6 33773 0.964 5.39 0.578 37 :2@C6_:1@C5 33759 0.964 4.19 0.772 38 :2@C6_:1@N3 33752 0.964 5.08 0.752 39 :2@C2_:1@N1 33716 0.963 4.26 0.782 40 :2@C4_:1@N2 33693 0.962 5.07 0.864 41 :2@N1_:1@N3 33684 0.962 5.22 0.747 42 :2@C4_:1@N7 33644 0.961 4.85 0.776 43 :2@N7_:1@N3 33628 0.96 4.97 0.799 44 :2@C5_:1@N7 33613 0.96 4.48 0.86 45 :2@C5_:1@C8 33575 0.959 4.47 0.844 46 :2@N3_:1@N2 33572 0.959 4.85 0.884 47 :2@C4_:1@C8 33569 0.959 4.93 0.772 48 :2@N1_:1@C6 33522 0.957 4.16 0.822 49 :2@N3_:1@O6 33495 0.956 4.68 0.743 50 :2@N9_:1@N2 33492 0.956 5.17 0.758 51 :2@C6_:1@N7 33472 0.956 4.15 0.866 52 :2@C8_:1@N9 33451 0.955 4.75 0.82 53 :2@C2_:1@O6 33450 0.955 4.18 0.814 54 :2@C5_:1@C2 33434 0.955 4.95 0.845 55 :2@N3_:1@N9 33424 0.954 5.07 0.735 56 :2@N1_:1@N7 33316 0.951 4.25 0.826 57 :2@C6_:1@C8 33286 0.95 4.38 0.812 58 :2@N7_:1@N9 33282 0.95 4.44 0.842 59 :2@C8_:1@C2 33126 0.946 5.37 0.755 60 :2@C4_:1@O6 33120 0.946 5.2 0.661 61 :2@N1_:1@N9 33041 0.943 5.04 0.671 62 :2@C2_:1@N7 33018 0.943 4.58 0.883 63 :2@N6_:1@C4 32986 0.942 5.02 0.742 64 :2@C5_:1@C6 32982 0.942 4.72 0.768 65 :2@N6_:1@N9 32859 0.938 4.95 0.695 66 :2@C8_:1@C5 32859 0.938 5.27 0.74 67 :2@N3_:1@N7 32829 0.937 4.9 0.844 68 :2@N1_:1@O6 32728 0.935 4.21 0.855 69 :2@N1_:1@N1 32718 0.934 4.59 0.915 70 :2@C6_:1@C6 32677 0.933 4.43 0.84 71 :2@N9_:1@C8 32663 0.933 5.38 0.756 72 :2@C2_:1@N9 32602 0.931 5.15 0.773 73 :2@N1_:1@C2 32596 0.931 5.07 0.9 74 :2@N1_:1@C8 32589 0.931 4.71 0.809 75 :2@N6_:1@N7 32496 0.928 4.2 0.953 76 :2@N7_:1@C5 32466 0.927 4.87 0.827 77 :2@N7_:1@C8 32452 0.927 4.62 0.95 78 :2@N6_:1@C5 32373 0.924 4.54 0.845 79 :2@N6_:1@C8 32365 0.924 4.4 0.847 80 :2@N9_:1@N7 32340 0.923 5.49 0.737 81 :2@C5_:1@N1 32316 0.923 4.94 0.814 82 :2@C8_:1@C8 32147 0.918 5.17 0.862 83 :2@N3_:1@C8 31887 0.911 5.19 0.812 84 :2@C2_:1@C8 31862 0.91 5.03 0.883 85 :2@C6_:1@C2 31782 0.908 5.13 0.899 86 :2@N7_:1@N7 31609 0.903 4.89 0.888 87 :2@C6_:1@N1 31465 0.898 4.84 0.903 88 :2@C6_:1@O6 31162 0.89 4.64 0.778 89 :2@N7_:1@C2 31050 0.887 5.38 0.815 90 :2@C5_:1@O6 30811 0.88 5.16 0.669 91 :2@C8_:1@N7 30610 0.874 5.45 0.767 92 :2@C8_:1@N1 30466 0.87 5.71 0.67 93 :2@N6_:1@C6 30351 0.867 4.81 0.862 94 :2@C8_:1@C6 30286 0.865 5.73 0.623 95 :2@N7_:1@C6 30160 0.861 5.39 0.726 96 :2@N9_:1@O6 30124 0.86 6 0.552 97 :2@C8_:1@N2 29969 0.856 5.73 0.798 98 :2@N6_:1@N3 29937 0.855 5.62 0.763 99 :2@N7_:1@N1 29517 0.843 5.57 0.792 100 :2@C5_:1@N2 29472 0.842 5.48 0.871 101 :2@N6_:1@O6 29403 0.84 4.92 0.892 102 :2@N6_:1@N1 27846 0.795 5.34 0.945 103 :2@N7_:1@O6 26753 0.764 5.93 0.697 104 :2@N6_:1@C2 25663 0.733 5.58 0.881 105 :2@N7_:1@N2 25327 0.723 5.8 0.841 106 :2@C6_:1@N2 24865 0.71 5.57 0.905 107 :2@C8_:1@O6 22754 0.65 6.25 0.562 108 :2@N6_:1@N2 15809 0.451 5.77 1.02 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 35021, 'v_base2' size 35021, output size 35021 TIME: Analyses took 0.0052 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 35021 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 35021 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 35021 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 35021 COM "COM" (double, distance), size is 35021 v_base1 "v_base1" (vector, vector), size is 35021 v_base2 "v_base2" (vector, vector), size is 35021 normalangle "normalangle" (double), size is 35021 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.6852 s ( 99.18%) TIME: Action Post : 0.0003 s ( 0.05%) TIME: Analysis : 0.0052 s ( 0.75%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6909 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: 0.8361 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.