CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 13:09:27 | Available memory: 1.218 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 :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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 14326 of 14326) Coordinate processing will occur on 14326 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.c2 (1-14326, 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 86 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@C6' to ':2@O2' 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@O6' to ':2@C2' Atom ':1@O6' to ':2@O2' 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@N1' to ':2@O2' 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@N2' to ':2@O2' 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 14326 frames and processed 14326 frames. TIME: Avg. throughput= 61415.1287 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 75.2669 86 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 14269 0.996 4.41 0.577 2 :1@N9_:2@C6 14248 0.995 4.78 0.553 3 :1@C4_:2@C5 14241 0.994 4.23 0.667 4 :1@N9_:2@C4 14195 0.991 4.75 0.662 5 :1@C4_:2@C4 14187 0.99 4.22 0.656 6 :1@C4_:2@O4 14160 0.988 4.27 0.72 7 :1@N3_:2@C5 14135 0.987 4.31 0.705 8 :1@C4_:2@C6 14133 0.987 4.79 0.674 9 :1@N3_:2@C4 14117 0.985 4.08 0.642 10 :1@N9_:2@N1 14105 0.985 5.42 0.505 11 :1@N9_:2@O4 14080 0.983 4.96 0.754 12 :1@N3_:2@O4 14079 0.983 4.22 0.699 13 :1@C5_:2@O4 14048 0.981 4.15 0.891 14 :1@C5_:2@C4 14019 0.979 4.41 0.816 15 :1@N3_:2@N3 13983 0.976 4.29 0.768 16 :1@C4_:2@N3 13969 0.975 4.72 0.766 17 :1@N3_:2@C6 13948 0.974 4.74 0.728 18 :1@C8_:2@C5 13931 0.972 4.74 0.708 19 :1@C6_:2@O4 13833 0.966 3.92 0.949 20 :1@C4_:2@N1 13831 0.965 5.29 0.6 21 :1@N3_:2@C2 13817 0.964 4.74 0.766 22 :1@C5_:2@C5 13816 0.964 4.49 0.746 23 :1@C2_:2@O4 13780 0.962 3.93 0.693 24 :1@N3_:2@N1 13776 0.962 4.96 0.709 25 :1@C8_:2@C6 13757 0.96 5.28 0.632 26 :1@C2_:2@C4 13737 0.959 4.04 0.665 27 :1@N9_:2@N3 13687 0.955 5.26 0.752 28 :1@N7_:2@C5 13668 0.954 4.84 0.758 29 :1@C2_:2@N3 13657 0.953 4.21 0.825 30 :1@N1_:2@O4 13649 0.953 3.78 0.756 31 :1@C8_:2@C4 13610 0.95 5.11 0.752 32 :1@C6_:2@C4 13578 0.948 4.43 0.84 33 :1@C4_:2@C2 13559 0.946 5.22 0.662 34 :1@C2_:2@C5 13531 0.945 4.57 0.703 35 :1@N1_:2@C4 13497 0.942 4.21 0.728 36 :1@N2_:2@O4 13470 0.94 4.32 0.772 37 :1@N2_:2@C4 13408 0.936 4.37 0.683 38 :1@N2_:2@N3 13358 0.932 4.24 0.82 39 :1@C8_:2@O4 13358 0.932 5.11 0.837 40 :1@N9_:2@C2 13354 0.932 5.59 0.628 41 :1@N1_:2@C5 13315 0.929 4.86 0.728 42 :1@N7_:2@O4 13272 0.926 4.68 0.829 43 :1@C5_:2@C6 13235 0.924 5.27 0.631 44 :1@C2_:2@C2 13223 0.923 4.86 0.846 45 :1@N7_:2@C4 13215 0.922 4.93 0.717 46 :1@C2_:2@C6 13202 0.922 5.19 0.736 47 :1@C6_:2@C5 13186 0.92 4.83 0.706 48 :1@N2_:2@C5 13180 0.92 5.07 0.778 49 :1@N1_:2@N3 13173 0.92 4.57 0.842 50 :1@C5_:2@N3 13109 0.915 5.01 0.702 51 :1@C2_:2@N1 12945 0.904 5.32 0.766 52 :1@O6_:2@O4 12911 0.901 4.16 0.852 53 :1@N2_:2@C2 12907 0.901 4.77 0.922 54 :1@N7_:2@C6 12879 0.899 5.56 0.61 55 :1@N3_:2@O2 12864 0.898 5.22 0.8 56 :1@C6_:2@N3 12658 0.884 4.96 0.708 57 :1@C8_:2@N1 12525 0.874 6.02 0.508 58 :1@O6_:2@C4 12401 0.866 4.86 0.674 59 :1@N2_:2@C6 12364 0.863 5.51 0.758 60 :1@N1_:2@C6 12349 0.862 5.65 0.678 61 :1@N2_:2@N1 12313 0.859 5.39 0.831 62 :1@O6_:2@C5 12305 0.859 5.44 0.65 63 :1@C5_:2@C2 12294 0.858 5.73 0.57 64 :1@C5_:2@N1 12216 0.853 5.85 0.512 65 :1@C6_:2@C6 12188 0.851 5.72 0.605 66 :1@N7_:2@N3 12159 0.849 5.68 0.656 67 :1@N1_:2@C2 12063 0.842 5.36 0.727 68 :1@C8_:2@N3 12053 0.841 5.71 0.694 69 :1@C2_:2@O2 12017 0.839 5.19 0.828 70 :1@N2_:2@O2 11892 0.83 4.86 0.981 71 :1@C4_:2@O2 11887 0.83 5.81 0.646 72 :1@O6_:2@N3 11799 0.824 5.56 0.664 73 :1@C6_:2@C2 11566 0.807 5.84 0.595 74 :1@N1_:2@N1 11202 0.782 5.85 0.661 75 :1@C8_:2@C2 10751 0.75 6.12 0.576 76 :1@N7_:2@N1 10710 0.748 6.26 0.462 77 :1@N1_:2@O2 10565 0.737 5.76 0.706 78 :1@C6_:2@N1 10536 0.735 6.14 0.525 79 :1@N7_:2@C2 10019 0.699 6.27 0.53 80 :1@N9_:2@O2 10012 0.699 6.09 0.657 81 :1@C5_:2@O2 8821 0.616 6.25 0.539 82 :1@C6_:2@O2 8039 0.561 6.24 0.517 83 :1@O6_:2@C2 7584 0.529 6.31 0.484 84 :1@C8_:2@O2 4409 0.308 6.3 0.749 85 :1@O6_:2@O2 3249 0.227 6.49 0.399 86 :1@N7_:2@O2 3134 0.219 6.36 0.72 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 14326, 'v_base2' size 14326, output size 14326 TIME: Analyses took 0.0020 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 14326 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 14326 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 14326 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 14326 COM "COM" (double, distance), size is 14326 v_base2 "v_base2" (vector, vector), size is 14326 v_base1 "v_base1" (vector, vector), size is 14326 normalangle "normalangle" (double), size is 14326 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.2333 s ( 99.02%) TIME: Action Post : 0.0003 s ( 0.12%) TIME: Analysis : 0.0020 s ( 0.83%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2356 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: 0.3098 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.