CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:02:43 | Available memory: 1.737 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,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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, 64 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 11408 of 11408) Coordinate processing will occur on 11408 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*](40) Reference mask: [:1,2&!@H*](40) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 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.c2 (1-11408, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 88 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@N4' 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@O6' to ':1@N1' Atom ':2@O6' to ':1@C6' Atom ':2@O6' to ':1@C5' Atom ':2@O6' to ':1@C4' Atom ':2@O6' to ':1@N4' Atom ':2@O6' to ':1@N3' Atom ':2@O6' to ':1@C2' Atom ':2@O6' 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@N2' to ':1@N1' Atom ':2@N2' to ':1@C6' Atom ':2@N2' to ':1@C5' Atom ':2@N2' to ':1@C4' Atom ':2@N2' to ':1@N4' Atom ':2@N2' to ':1@N3' Atom ':2@N2' to ':1@C2' Atom ':2@N2' 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 11408 frames and processed 11408 frames. TIME: Avg. throughput= 62366.4026 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 78.5379 88 # Contact Nframes Frac. Avg Stdev 1 :2@C4_:1@N1 10840 0.95 4.89 0.595 2 :2@N9_:1@N1 10820 0.948 5.3 0.656 3 :2@C4_:1@C6 10815 0.948 4.66 0.676 4 :2@C5_:1@N1 10809 0.947 5.02 0.72 5 :2@N9_:1@C6 10762 0.943 4.97 0.654 6 :2@C5_:1@C6 10723 0.94 4.85 0.673 7 :2@C5_:1@C2 10723 0.94 4.88 0.854 8 :2@C6_:1@C2 10691 0.937 4.77 0.742 9 :2@C4_:1@C5 10681 0.936 4.44 0.796 10 :2@N3_:1@C6 10674 0.936 4.63 0.826 11 :2@N3_:1@N1 10667 0.935 4.79 0.774 12 :2@C6_:1@N1 10656 0.934 5.15 0.606 13 :2@C6_:1@N3 10651 0.934 4.31 0.828 14 :2@C4_:1@C2 10649 0.933 4.89 0.738 15 :2@C5_:1@N3 10625 0.931 4.59 0.861 16 :2@C6_:1@C6 10612 0.93 5.07 0.726 17 :2@C5_:1@C5 10609 0.93 4.52 0.765 18 :2@C6_:1@C4 10602 0.929 4.24 0.788 19 :2@C5_:1@C4 10583 0.928 4.4 0.805 20 :2@N1_:1@N1 10570 0.927 5.03 0.651 21 :2@C6_:1@C5 10568 0.926 4.63 0.81 22 :2@C2_:1@C6 10562 0.926 4.8 0.846 23 :2@N1_:1@C6 10543 0.924 5.02 0.76 24 :2@N1_:1@C2 10542 0.924 4.57 0.73 25 :2@C8_:1@C6 10537 0.924 5.28 0.741 26 :2@N3_:1@C5 10534 0.923 4.44 0.768 27 :2@N1_:1@C4 10526 0.923 4.13 0.777 28 :2@N7_:1@C6 10522 0.922 5.23 0.829 29 :2@N1_:1@N3 10520 0.922 4.1 0.792 30 :2@C2_:1@N1 10519 0.922 4.81 0.862 31 :2@N9_:1@C5 10515 0.922 4.84 0.794 32 :2@C2_:1@C5 10514 0.922 4.51 0.768 33 :2@N1_:1@C5 10513 0.922 4.6 0.803 34 :2@C4_:1@C4 10509 0.921 4.47 0.776 35 :2@C4_:1@N3 10495 0.92 4.69 0.803 36 :2@N3_:1@C2 10492 0.92 4.75 0.76 37 :2@O6_:1@C2 10490 0.92 5.16 0.783 38 :2@O6_:1@N3 10474 0.918 4.62 0.782 39 :2@C2_:1@C2 10423 0.914 4.52 0.836 40 :2@O6_:1@C4 10408 0.912 4.61 0.75 41 :2@C2_:1@N3 10373 0.909 4.21 0.756 42 :2@N3_:1@N3 10365 0.909 4.56 0.758 43 :2@C2_:1@C4 10364 0.908 4.18 0.693 44 :2@C6_:1@O2 10323 0.905 5.13 0.928 45 :2@N3_:1@C4 10321 0.905 4.39 0.674 46 :2@C6_:1@N4 10308 0.904 4.23 0.903 47 :2@O6_:1@N1 10302 0.903 5.65 0.705 48 :2@N1_:1@N4 10272 0.9 4.15 0.817 49 :2@N7_:1@C5 10256 0.899 4.94 0.755 50 :2@N2_:1@C4 10246 0.898 4.61 0.716 51 :2@N1_:1@O2 10235 0.897 4.91 0.841 52 :2@N2_:1@C5 10233 0.897 4.96 0.777 53 :2@O6_:1@C5 10230 0.897 5.1 0.892 54 :2@N9_:1@C4 10210 0.895 5.09 0.735 55 :2@N7_:1@C4 10192 0.893 4.94 0.775 56 :2@N2_:1@N3 10189 0.893 4.53 0.78 57 :2@C8_:1@C5 10173 0.892 5.09 0.731 58 :2@C2_:1@N4 10163 0.891 4.35 0.773 59 :2@C5_:1@N4 10153 0.89 4.5 0.893 60 :2@O6_:1@N4 10141 0.889 4.44 0.945 61 :2@N7_:1@N1 10121 0.887 5.34 1.03 62 :2@O6_:1@C6 10108 0.886 5.6 0.857 63 :2@N3_:1@N4 10098 0.885 4.68 0.742 64 :2@C4_:1@O2 10091 0.885 5.37 0.841 65 :2@N9_:1@C2 10091 0.885 5.41 0.775 66 :2@C8_:1@N1 10066 0.882 5.46 0.944 67 :2@C4_:1@N4 10053 0.881 4.72 0.777 68 :2@N2_:1@N4 10038 0.88 4.72 0.961 69 :2@N7_:1@N3 10030 0.879 5.15 0.873 70 :2@N3_:1@O2 10019 0.878 5.2 0.805 71 :2@C2_:1@O2 9987 0.875 4.88 0.885 72 :2@N2_:1@C6 9931 0.871 5.14 0.941 73 :2@N9_:1@N3 9930 0.87 5.35 0.751 74 :2@C8_:1@C4 9915 0.869 5.28 0.731 75 :2@N2_:1@C2 9878 0.866 4.68 1.01 76 :2@C5_:1@O2 9862 0.864 5.24 0.972 77 :2@N7_:1@C2 9759 0.855 5.26 1.04 78 :2@O6_:1@O2 9683 0.849 5.34 1.05 79 :2@N7_:1@N4 9646 0.846 5.01 0.958 80 :2@N9_:1@N4 9453 0.829 5.34 0.749 81 :2@N2_:1@N1 9449 0.828 4.91 1.05 82 :2@C8_:1@N3 9350 0.82 5.48 0.782 83 :2@C8_:1@N4 9126 0.8 5.43 0.859 84 :2@N2_:1@O2 9070 0.795 4.79 1.07 85 :2@C8_:1@C2 9068 0.795 5.47 0.942 86 :2@N9_:1@O2 8050 0.706 5.64 0.898 87 :2@N7_:1@O2 7519 0.659 5.21 1.08 88 :2@C8_:1@O2 6552 0.574 5.36 0.92 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 11408, 'v_base2' size 11408, output size 11408 TIME: Analyses took 0.0015 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 11408 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 11408 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 11408 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 11408 COM "COM" (double, distance), size is 11408 v_base2 "v_base2" (vector, vector), size is 11408 v_base1 "v_base1" (vector, vector), size is 11408 normalangle "normalangle" (double), size is 11408 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1829 s ( 98.99%) TIME: Action Post : 0.0003 s ( 0.14%) TIME: Analysis : 0.0015 s ( 0.82%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1848 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: 0.2452 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.