CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 14:33:45 | Available memory: 1.701 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,C6,C5,C4,N4,N3,C2,O2 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,C6,C5,C4,N4,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_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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [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] [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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 (1 total): 0: [traj] noWAt.topo.hmr, 63 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 172040 of 172040) Coordinate processing will occur on 172040 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*](39) Reference mask: [:1,2&!@H*](39) 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,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base2 :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_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-172040, 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,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 79 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C4' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@O2' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C4' Atom ':2@C8' to ':1@N4' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@O2' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C4' Atom ':2@N7' to ':1@N4' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@N4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@N4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C4' Atom ':2@N6' to ':1@N4' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@O2' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@N4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@N4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@N4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@N4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 172040 frames and processed 172040 frames. TIME: Avg. throughput= 97861.9296 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 70.5603 79 # Contact Nframes Frac. Avg Stdev 1 :2@N7_:1@N1 170090 0.989 4.67 0.687 2 :2@N7_:1@C2 169592 0.986 4.75 0.849 3 :2@C5_:1@C2 169476 0.985 4.46 0.629 4 :2@C8_:1@N1 169440 0.985 5.14 0.682 5 :2@C5_:1@O2 169195 0.983 4.6 0.773 6 :2@C5_:1@N1 168785 0.981 4.5 0.584 7 :2@N9_:1@N1 168158 0.977 5.36 0.513 8 :2@C6_:1@O2 168067 0.977 4.45 0.785 9 :2@N6_:1@O2 167692 0.975 4.66 0.871 10 :2@N6_:1@C2 167433 0.973 4.27 0.716 11 :2@C4_:1@O2 167400 0.973 4.93 0.762 12 :2@C6_:1@C2 167296 0.972 4.21 0.659 13 :2@C4_:1@C2 166913 0.97 4.95 0.611 14 :2@C5_:1@N3 166788 0.969 4.74 0.726 15 :2@N9_:1@C2 166326 0.967 5.55 0.646 16 :2@N6_:1@N3 166218 0.966 3.92 0.743 17 :2@N7_:1@C6 165880 0.964 4.87 0.829 18 :2@N7_:1@N3 165836 0.964 5.08 0.925 19 :2@C4_:1@N1 165667 0.963 4.9 0.547 20 :2@N7_:1@O2 165534 0.962 4.91 1 21 :2@C8_:1@C2 165481 0.962 5.34 0.824 22 :2@C6_:1@N3 165161 0.96 4.19 0.693 23 :2@C6_:1@N1 164378 0.955 4.44 0.669 24 :2@N9_:1@O2 164100 0.954 5.47 0.805 25 :2@N6_:1@N1 164033 0.953 4.62 0.691 26 :2@N6_:1@C4 163604 0.951 3.93 0.738 27 :2@C5_:1@C6 162894 0.947 4.75 0.69 28 :2@C5_:1@C4 162288 0.943 4.99 0.659 29 :2@N7_:1@C4 162032 0.942 5.27 0.849 30 :2@C6_:1@C4 161707 0.94 4.38 0.685 31 :2@N1_:1@C2 161652 0.94 4.42 0.821 32 :2@N6_:1@N4 161531 0.939 4.16 0.801 33 :2@N1_:1@O2 160937 0.935 4.52 0.911 34 :2@C4_:1@N3 160788 0.935 5.42 0.664 35 :2@C8_:1@C6 160633 0.934 5.42 0.738 36 :2@N6_:1@C6 160484 0.933 4.58 0.855 37 :2@C6_:1@C6 160240 0.931 4.61 0.822 38 :2@N6_:1@C5 160216 0.931 4.25 0.869 39 :2@N1_:1@N3 160008 0.93 4.4 0.843 40 :2@N1_:1@N1 159892 0.929 4.76 0.88 41 :2@C5_:1@C5 159438 0.927 5 0.663 42 :2@N3_:1@C2 158969 0.924 5.17 0.706 43 :2@N7_:1@C5 158837 0.923 5.13 0.815 44 :2@N3_:1@O2 158546 0.922 5.02 0.877 45 :2@C6_:1@C5 158408 0.921 4.58 0.786 46 :2@N3_:1@N1 158370 0.921 5.22 0.696 47 :2@C4_:1@C6 158362 0.92 5.3 0.64 48 :2@C2_:1@C2 158053 0.919 4.84 0.857 49 :2@C6_:1@N4 157607 0.916 4.84 0.72 50 :2@N9_:1@C6 157026 0.913 5.77 0.572 51 :2@C8_:1@O2 156111 0.907 5.3 0.943 52 :2@C2_:1@N1 155903 0.906 5.06 0.88 53 :2@N1_:1@C4 155894 0.906 4.67 0.853 54 :2@C2_:1@O2 154735 0.899 4.71 0.957 55 :2@C4_:1@C4 153019 0.889 5.77 0.581 56 :2@C2_:1@N3 152958 0.889 5.05 0.842 57 :2@C5_:1@N4 152937 0.889 5.61 0.681 58 :2@C4_:1@C5 150951 0.877 5.72 0.596 59 :2@N1_:1@C6 150114 0.873 4.92 1.01 60 :2@N1_:1@N4 150019 0.872 5.06 0.832 61 :2@N3_:1@N3 149643 0.87 5.59 0.698 62 :2@N1_:1@C5 148650 0.864 4.88 0.976 63 :2@C2_:1@C4 144707 0.841 5.4 0.799 64 :2@C8_:1@N3 143342 0.833 5.73 0.795 65 :2@C8_:1@C5 142126 0.826 5.83 0.696 66 :2@N3_:1@C6 140141 0.815 5.55 0.759 67 :2@N9_:1@N3 139125 0.809 6.03 0.641 68 :2@N7_:1@N4 136851 0.795 5.77 0.777 69 :2@C2_:1@C6 135381 0.787 5.22 0.923 70 :2@N3_:1@C4 134235 0.78 5.95 0.609 71 :2@C8_:1@C4 130984 0.761 5.95 0.701 72 :2@C2_:1@C5 130881 0.761 5.41 0.875 73 :2@N9_:1@C5 128905 0.749 6.23 0.524 74 :2@N3_:1@C5 125616 0.73 5.89 0.678 75 :2@C2_:1@N4 123316 0.717 5.8 0.705 76 :2@N9_:1@C4 111845 0.65 6.27 0.517 77 :2@C4_:1@N4 108769 0.632 6.26 0.524 78 :2@N3_:1@N4 83446 0.485 6.3 0.506 79 :2@C8_:1@N4 71127 0.413 6.23 0.55 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 172040, 'v_base2' size 172040, output size 172040 TIME: Analyses took 0.0151 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 172040 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 172040 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 172040 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 172040 COM "COM" (double, distance), size is 172040 v_base2 "v_base2" (vector, vector), size is 172040 v_base1 "v_base1" (vector, vector), size is 172040 normalangle "normalangle" (double), size is 172040 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.11%) TIME: Trajectory Process : 1.7580 s ( 99.02%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0151 s ( 0.85%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 1.7754 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: 2.2651 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.