CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:32:58 | Available memory: 1.233 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.c3] Reading '../ctraj.c3' 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@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, 67 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 105630 of 105630) Coordinate processing will occur on 105630 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :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. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c3 (1-105630, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 96 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@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@O6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N2' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C4' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@N9' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@N2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' to ':2@C4' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' 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@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 105630 frames and processed 105630 frames. TIME: Avg. throughput= 82078.4186 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 80.1434 96 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 96759 0.916 5.06 0.747 2 :1@C4_:2@N9 96711 0.916 5.14 0.675 3 :1@C2_:2@N9 94877 0.898 5.05 0.802 4 :1@N3_:2@C4 93948 0.889 4.62 0.715 5 :1@C4_:2@C4 93881 0.889 4.67 0.671 6 :1@N1_:2@N9 93240 0.883 5.18 0.682 7 :1@N3_:2@N3 93180 0.882 4.67 0.85 8 :1@C2_:2@C4 93176 0.882 4.53 0.774 9 :1@C5_:2@N9 93027 0.881 5.17 0.813 10 :1@C2_:2@N3 93023 0.881 4.58 0.838 11 :1@C5_:2@C4 93003 0.88 4.67 0.778 12 :1@N1_:2@N3 92921 0.88 4.6 0.785 13 :1@N1_:2@C4 92911 0.88 4.57 0.728 14 :1@C4_:2@C8 92877 0.879 5.25 0.854 15 :1@C6_:2@C4 92639 0.877 4.66 0.745 16 :1@C4_:2@N3 92542 0.876 4.72 0.768 17 :1@N3_:2@C8 92467 0.875 5.2 0.842 18 :1@C6_:2@N3 92400 0.875 4.71 0.743 19 :1@C6_:2@N9 92375 0.875 5.26 0.761 20 :1@N9_:2@N9 92010 0.871 5.5 0.667 21 :1@C4_:2@C5 91810 0.869 4.61 0.733 22 :1@C5_:2@N3 91726 0.868 4.73 0.725 23 :1@N1_:2@C2 91585 0.867 4.4 0.761 24 :1@N9_:2@C4 91430 0.866 5.19 0.657 25 :1@C2_:2@C2 91414 0.865 4.5 0.823 26 :1@C6_:2@C2 91343 0.865 4.48 0.818 27 :1@N3_:2@C5 91283 0.864 4.61 0.657 28 :1@C5_:2@C5 90972 0.861 4.52 0.805 29 :1@C2_:2@C5 90808 0.86 4.45 0.728 30 :1@N1_:2@N1 90756 0.859 4.23 0.71 31 :1@N1_:2@C5 90590 0.858 4.37 0.801 32 :1@C5_:2@C2 90535 0.857 4.61 0.773 33 :1@C2_:2@N1 90513 0.857 4.43 0.821 34 :1@N3_:2@C2 90461 0.856 4.65 0.937 35 :1@C2_:2@C8 90449 0.856 5.22 0.793 36 :1@N3_:2@C6 90393 0.856 4.72 0.684 37 :1@C4_:2@C2 90336 0.855 4.68 0.84 38 :1@C2_:2@C6 90319 0.855 4.44 0.805 39 :1@C6_:2@C5 90250 0.854 4.43 0.803 40 :1@C6_:2@N1 90229 0.854 4.25 0.797 41 :1@N1_:2@C6 90227 0.854 4.22 0.811 42 :1@N3_:2@N1 90021 0.852 4.7 0.852 43 :1@N1_:2@N2 90004 0.852 4.85 0.925 44 :1@C4_:2@C6 89961 0.852 4.67 0.678 45 :1@C4_:2@N1 89940 0.851 4.69 0.748 46 :1@C4_:2@N7 89932 0.851 4.98 0.931 47 :1@C5_:2@N1 89894 0.851 4.47 0.823 48 :1@N2_:2@C4 89697 0.849 4.84 0.894 49 :1@C6_:2@C6 89522 0.848 4.23 0.76 50 :1@C5_:2@C6 89432 0.847 4.43 0.782 51 :1@O6_:2@N3 89370 0.846 5.1 0.837 52 :1@O6_:2@C2 89160 0.844 4.78 1.02 53 :1@N3_:2@N7 89108 0.844 4.98 0.828 54 :1@N9_:2@C5 89084 0.843 5.15 0.791 55 :1@O6_:2@C4 88938 0.842 5.07 0.757 56 :1@C6_:2@N2 88764 0.84 4.9 0.971 57 :1@O6_:2@N1 88675 0.839 4.49 0.977 58 :1@N2_:2@C5 88662 0.839 4.84 0.852 59 :1@N2_:2@N1 88274 0.836 4.8 1.03 60 :1@N2_:2@C2 88267 0.836 4.84 0.887 61 :1@N2_:2@N3 88207 0.835 4.84 0.903 62 :1@N3_:2@O6 88140 0.834 5.19 0.743 63 :1@N9_:2@N3 87897 0.832 5.18 0.818 64 :1@N2_:2@N9 87604 0.829 5.2 1.02 65 :1@N7_:2@C4 87472 0.828 5.1 0.878 66 :1@C4_:2@O6 87252 0.826 5.08 0.717 67 :1@C2_:2@N2 87175 0.825 4.9 0.847 68 :1@C5_:2@N2 87131 0.825 5.05 0.841 69 :1@N9_:2@C6 86861 0.822 5.28 0.776 70 :1@N7_:2@C5 86836 0.822 4.98 0.881 71 :1@C5_:2@O6 86528 0.819 4.74 0.832 72 :1@N7_:2@C2 86270 0.817 5.11 0.839 73 :1@N7_:2@N3 86107 0.815 5.18 0.8 74 :1@N7_:2@N1 86050 0.815 4.96 1 75 :1@C8_:2@C4 85970 0.814 5.35 0.803 76 :1@N7_:2@C6 85952 0.814 4.89 0.995 77 :1@N9_:2@N1 84591 0.801 5.27 0.712 78 :1@C8_:2@C5 84034 0.796 5.25 0.849 79 :1@N9_:2@C2 83650 0.792 5.15 0.838 80 :1@C4_:2@N2 83574 0.791 5.01 0.922 81 :1@C8_:2@N3 82969 0.785 5.37 0.813 82 :1@N9_:2@C8 82957 0.785 5.42 0.828 83 :1@N2_:2@C8 82912 0.785 5.39 0.945 84 :1@C8_:2@C6 82445 0.781 5.29 0.963 85 :1@N3_:2@N2 82424 0.78 4.92 0.98 86 :1@N2_:2@N2 82055 0.777 5.13 0.883 87 :1@C8_:2@N1 81860 0.775 5.35 0.872 88 :1@C8_:2@C2 81707 0.774 5.37 0.805 89 :1@N7_:2@N2 80055 0.758 5.44 0.908 90 :1@N9_:2@N7 79916 0.757 5.2 0.974 91 :1@O6_:2@N2 79505 0.753 4.89 1.21 92 :1@N7_:2@O6 78811 0.746 4.97 1.14 93 :1@N9_:2@O6 77971 0.738 5.54 0.897 94 :1@N9_:2@N2 70562 0.668 5.2 0.978 95 :1@C8_:2@N2 70221 0.665 5.5 0.917 96 :1@C8_:2@O6 69780 0.661 5.27 1.14 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 105630, 'v_base2' size 105630, output size 105630 TIME: Analyses took 0.0075 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 105630 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 105630 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 105630 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 105630 COM "COM" (double, distance), size is 105630 v_base1 "v_base1" (vector, vector), size is 105630 v_base2 "v_base2" (vector, vector), size is 105630 normalangle "normalangle" (double), size is 105630 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0009 s ( 0.07%) TIME: Trajectory Process : 1.2869 s ( 99.33%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0075 s ( 0.58%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.2956 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: 1.5682 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.