CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 15:13:48 | Available memory: 2.425 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.c1] Reading '../ctraj.c1' 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,C6,C5,C4,O4,N3,C2,O2 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,C6,C5,C4,O4,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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [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] [vector v_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,O4,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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 17391 of 17391) Coordinate processing will occur on 17391 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [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. 6: [vector v_base1 :2@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-17391, 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,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 82 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@O4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@O4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@O2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@O4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C4' Atom ':1@O6' to ':2@O4' Atom ':1@O6' to ':2@N3' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C4' Atom ':1@N2' to ':2@O4' Atom ':1@N2' to ':2@N3' Atom ':1@N2' to ':2@C2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 17391 frames and processed 17391 frames. TIME: Avg. throughput= 61420.1760 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 70.6653 82 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C6 17315 0.996 4.82 0.573 2 :1@N9_:2@C5 17301 0.995 4.51 0.631 3 :1@C4_:2@C5 17293 0.994 4.28 0.662 4 :1@C4_:2@C6 17228 0.991 4.84 0.653 5 :1@N9_:2@C4 17185 0.988 4.71 0.691 6 :1@C4_:2@C4 17182 0.988 4.41 0.696 7 :1@N9_:2@N1 17133 0.985 5.26 0.589 8 :1@N3_:2@C5 17125 0.985 4.26 0.755 9 :1@C4_:2@O4 17083 0.982 4.46 0.773 10 :1@C5_:2@C4 17045 0.98 4.47 0.849 11 :1@C5_:2@O4 17023 0.979 4.26 0.925 12 :1@N3_:2@C6 17020 0.979 4.83 0.713 13 :1@C5_:2@C5 16958 0.975 4.61 0.745 14 :1@N3_:2@C4 16927 0.973 4.55 0.815 15 :1@N9_:2@O4 16924 0.973 4.95 0.783 16 :1@C4_:2@N1 16839 0.968 5.45 0.657 17 :1@C6_:2@O4 16823 0.967 4.22 1.05 18 :1@C8_:2@C5 16802 0.966 4.89 0.8 19 :1@N3_:2@O4 16749 0.963 4.58 0.892 20 :1@C2_:2@C5 16722 0.962 4.53 0.882 21 :1@C4_:2@N3 16720 0.961 4.98 0.823 22 :1@C6_:2@C4 16655 0.958 4.69 0.956 23 :1@C8_:2@C6 16648 0.957 5.28 0.683 24 :1@N9_:2@N3 16626 0.956 5.04 0.776 25 :1@C8_:2@C4 16535 0.951 4.81 0.873 26 :1@N7_:2@C5 16459 0.946 4.97 0.774 27 :1@C5_:2@C6 16447 0.946 5.33 0.688 28 :1@C6_:2@C5 16409 0.944 4.94 0.791 29 :1@N1_:2@C5 16403 0.943 4.87 0.875 30 :1@N9_:2@C2 16286 0.936 5.3 0.71 31 :1@N1_:2@O4 16214 0.932 4.22 1.01 32 :1@N7_:2@C4 16141 0.928 4.67 0.83 33 :1@N3_:2@N1 16124 0.927 5.53 0.625 34 :1@C2_:2@C4 16074 0.924 4.58 0.868 35 :1@N7_:2@O4 16071 0.924 4.51 0.958 36 :1@C2_:2@C6 16038 0.922 5.28 0.763 37 :1@C8_:2@O4 16017 0.921 4.87 0.971 38 :1@C2_:2@O4 16004 0.92 4.34 0.956 39 :1@N1_:2@C4 15997 0.92 4.68 0.902 40 :1@C4_:2@C2 15916 0.915 5.43 0.748 41 :1@O6_:2@O4 15891 0.914 4.45 1.04 42 :1@C5_:2@N3 15857 0.912 4.94 0.879 43 :1@N3_:2@N3 15713 0.904 5.13 0.833 44 :1@C8_:2@N1 15691 0.902 5.51 0.678 45 :1@N7_:2@C6 15671 0.901 5.55 0.655 46 :1@N2_:2@C5 15620 0.898 4.84 0.916 47 :1@C8_:2@N3 15589 0.896 4.95 0.826 48 :1@N7_:2@N3 15370 0.884 4.94 0.87 49 :1@C8_:2@C2 15132 0.87 5.3 0.777 50 :1@O6_:2@C4 14977 0.861 5.03 0.868 51 :1@N3_:2@C2 14869 0.855 5.59 0.705 52 :1@O6_:2@C5 14859 0.854 5.52 0.699 53 :1@C5_:2@N1 14698 0.845 5.76 0.714 54 :1@N2_:2@O4 14604 0.84 4.62 1 55 :1@N2_:2@C4 14578 0.838 4.9 0.873 56 :1@C6_:2@C6 14542 0.836 5.74 0.663 57 :1@N1_:2@C6 14501 0.834 5.67 0.704 58 :1@C2_:2@N3 14483 0.833 5.25 0.802 59 :1@N2_:2@C6 14342 0.825 5.52 0.737 60 :1@C6_:2@N3 14339 0.825 5.15 0.857 61 :1@C5_:2@C2 14332 0.824 5.52 0.806 62 :1@N7_:2@C2 14266 0.82 5.48 0.851 63 :1@N1_:2@N3 14099 0.811 5.33 0.799 64 :1@N7_:2@N1 14066 0.809 5.79 0.707 65 :1@C2_:2@N1 13784 0.793 5.93 0.604 66 :1@N9_:2@O2 13554 0.779 5.72 0.771 67 :1@C2_:2@C2 12972 0.746 5.89 0.682 68 :1@C8_:2@O2 12913 0.743 5.59 0.87 69 :1@O6_:2@N3 12740 0.733 5.46 0.866 70 :1@N2_:2@N3 12498 0.719 5.56 0.893 71 :1@C4_:2@O2 12018 0.691 5.84 0.732 72 :1@C6_:2@C2 11887 0.684 5.85 0.762 73 :1@N1_:2@C2 11374 0.654 6.02 0.676 74 :1@N2_:2@N1 10990 0.632 6.17 0.586 75 :1@N7_:2@O2 10855 0.624 5.61 0.882 76 :1@N1_:2@N1 10808 0.621 6.18 0.628 77 :1@C6_:2@N1 10793 0.621 6.09 0.661 78 :1@C5_:2@O2 10598 0.609 5.81 0.788 79 :1@O6_:2@C6 10245 0.589 6.21 0.547 80 :1@N3_:2@O2 10155 0.584 6.03 0.768 81 :1@N2_:2@C2 9422 0.542 6.05 0.724 82 :1@C2_:2@O2 6784 0.39 6.12 0.723 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 17391, 'v_base2' size 17391, output size 17391 TIME: Analyses took 0.0023 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 17391 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 17391 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 17391 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 17391 COM "COM" (double, distance), size is 17391 v_base2 "v_base2" (vector, vector), size is 17391 v_base1 "v_base1" (vector, vector), size is 17391 normalangle "normalangle" (double), size is 17391 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.2831 s ( 99.08%) TIME: Action Post : 0.0003 s ( 0.09%) TIME: Analysis : 0.0023 s ( 0.80%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2858 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: 0.3760 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.