CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:24:02 | Available memory: 7.028 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 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,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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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_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] [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, 66 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 21614 of 21614) Coordinate processing will occur on 21614 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*](42) Reference mask: [:1,2&!@H*](42) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :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_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. ----- ctraj.c2 (1-21614, 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 72 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@N7' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C4' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@O6' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@O6' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 21614 frames and processed 21614 frames. TIME: Avg. throughput= 53357.0981 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 67.5365 72 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N9 21540 0.997 4.54 0.543 2 :2@N7_:1@N9 21516 0.995 4.86 0.774 3 :2@C5_:1@C4 21491 0.994 4.58 0.59 4 :2@N9_:1@N9 21478 0.994 5.31 0.542 5 :2@C4_:1@N9 21446 0.992 4.82 0.506 6 :2@C8_:1@N9 21393 0.99 5.26 0.752 7 :2@C4_:1@C4 21342 0.987 5.05 0.645 8 :2@C6_:1@N9 21340 0.987 4.51 0.625 9 :2@C6_:1@C4 21314 0.986 4.37 0.643 10 :2@N7_:1@C4 21292 0.985 4.88 0.811 11 :2@C5_:1@C5 21291 0.985 4.85 0.737 12 :2@N6_:1@C4 21285 0.985 4.46 0.679 13 :2@C5_:1@C8 21260 0.984 4.76 0.78 14 :2@N6_:1@C5 21219 0.982 4.19 0.773 15 :2@C6_:1@C5 21185 0.98 4.35 0.726 16 :2@N6_:1@N9 21173 0.98 4.8 0.731 17 :2@C5_:1@N3 21170 0.979 4.83 0.746 18 :2@C6_:1@C8 21144 0.978 4.52 0.841 19 :2@C4_:1@C8 21062 0.974 5.1 0.619 20 :2@C6_:1@N7 21047 0.974 4.47 0.83 21 :2@N3_:1@N9 21045 0.974 5.04 0.692 22 :2@N6_:1@C6 20941 0.969 4.3 0.883 23 :2@N1_:1@N9 20934 0.969 4.7 0.767 24 :2@C6_:1@N3 20918 0.968 4.69 0.832 25 :2@N9_:1@C4 20898 0.967 5.61 0.654 26 :2@C5_:1@N7 20816 0.963 4.94 0.787 27 :2@N6_:1@N7 20811 0.963 4.32 1 28 :2@N6_:1@N3 20811 0.963 4.75 0.906 29 :2@N1_:1@C4 20786 0.962 4.57 0.889 30 :2@C2_:1@N9 20756 0.96 4.91 0.815 31 :2@C4_:1@N3 20737 0.959 5.27 0.731 32 :2@N1_:1@C8 20722 0.959 4.62 0.876 33 :2@C6_:1@C6 20710 0.958 4.7 0.876 34 :2@N6_:1@C8 20672 0.956 4.63 0.999 35 :2@N1_:1@C5 20667 0.956 4.47 0.922 36 :2@C8_:1@C4 20615 0.954 5.41 0.815 37 :2@N1_:1@N7 20581 0.952 4.53 0.867 38 :2@C4_:1@C5 20517 0.949 5.42 0.703 39 :2@N6_:1@O6 20449 0.946 4.59 0.992 40 :2@N7_:1@C5 20447 0.946 5.19 0.916 41 :2@N3_:1@C8 20445 0.946 5.2 0.735 42 :2@N7_:1@C8 20390 0.943 5.09 0.987 43 :2@N7_:1@N3 20383 0.943 4.92 0.883 44 :2@N9_:1@C8 20370 0.942 5.68 0.624 45 :2@C2_:1@C8 20365 0.942 4.9 0.872 46 :2@N3_:1@C4 20256 0.937 5.24 0.802 47 :2@N6_:1@N1 20255 0.937 4.5 0.967 48 :2@C4_:1@N7 20211 0.935 5.45 0.645 49 :2@C5_:1@C6 20083 0.929 5.33 0.816 50 :2@C2_:1@C4 20073 0.929 4.92 0.945 51 :2@N6_:1@C2 19959 0.923 4.65 1.03 52 :2@C5_:1@C2 19868 0.919 5.18 0.819 53 :2@N9_:1@N3 19840 0.918 5.71 0.699 54 :2@C6_:1@C2 19829 0.917 4.83 0.917 55 :2@C6_:1@N1 19768 0.915 4.86 0.904 56 :2@C2_:1@N7 19750 0.914 5 0.878 57 :2@C2_:1@C5 19500 0.902 4.98 0.925 58 :2@C8_:1@N3 19482 0.901 5.39 0.861 59 :2@C6_:1@O6 19469 0.901 5.11 0.893 60 :2@C8_:1@C8 19426 0.899 5.56 0.85 61 :2@N1_:1@C6 19376 0.896 4.69 1 62 :2@N1_:1@N3 19323 0.894 4.82 0.963 63 :2@N7_:1@N7 19316 0.894 5.27 0.98 64 :2@N3_:1@N7 19251 0.891 5.5 0.742 65 :2@N3_:1@C5 18745 0.867 5.46 0.753 66 :2@N7_:1@C2 18732 0.867 5.22 0.94 67 :2@N7_:1@C6 18218 0.843 5.56 0.917 68 :2@N1_:1@O6 18057 0.835 5.01 0.93 69 :2@C8_:1@C5 17765 0.822 5.78 0.829 70 :2@N6_:1@N2 17266 0.799 4.96 1.16 71 :2@N9_:1@N7 17091 0.791 6.04 0.614 72 :2@C8_:1@N7 16050 0.743 5.78 0.807 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 21614, 'v_base2' size 21614, output size 21614 TIME: Analyses took 0.0031 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 21614 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 21614 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 21614 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 21614 COM "COM" (double, distance), size is 21614 v_base1 "v_base1" (vector, vector), size is 21614 v_base2 "v_base2" (vector, vector), size is 21614 normalangle "normalangle" (double), size is 21614 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.4051 s ( 99.14%) TIME: Action Post : 0.0003 s ( 0.06%) TIME: Analysis : 0.0031 s ( 0.77%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4086 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: 0.5094 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.