CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 14:44:40 | Available memory: 1.576 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.c4] Reading '../ctraj.c4' 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,C2,N3,C4,C5,C6,N6,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,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :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,N6,H61,H62,N7,C8,H8,N9 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,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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, 66 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c4' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 52258 of 52258) Coordinate processing will occur on 52258 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 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (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,N6,N7,C8,N9 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 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.c4 (1-52258, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 61 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@N9' Atom ':1@C8' to ':2@C8' Atom ':1@C8' to ':2@N7' 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@C4' Atom ':1@N7' to ':2@C8' Atom ':1@N7' to ':2@N7' 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@C5' to ':2@N7' 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@C6' to ':2@C6' Atom ':1@C6' to ':2@O6' Atom ':1@N6' to ':2@O6' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@O6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@O6' Atom ':1@C2' to ':2@N1' 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@N3' Atom ':1@C4' to ':2@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 52258 frames and processed 52258 frames. TIME: Avg. throughput= 95215.8838 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 42.4566 61 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N7 43778 0.838 5.3 0.748 2 :1@N9_:2@C5 43714 0.837 4.9 0.71 3 :1@N9_:2@C6 43218 0.827 4.51 0.846 4 :1@N9_:2@C4 42800 0.819 5.35 0.593 5 :1@N9_:2@O6 42757 0.818 4.49 0.931 6 :1@C4_:2@C6 42039 0.804 4.95 0.768 7 :1@N9_:2@N1 41998 0.804 4.63 0.878 8 :1@C4_:2@O6 41669 0.797 4.86 0.803 9 :1@C4_:2@C5 41625 0.797 5.44 0.636 10 :1@N9_:2@C8 41367 0.792 5.84 0.614 11 :1@C8_:2@C5 41235 0.789 5.21 0.779 12 :1@N3_:2@C6 41188 0.788 5.26 0.879 13 :1@C4_:2@N1 41123 0.787 4.98 0.863 14 :1@N9_:2@N3 41036 0.785 5.48 0.655 15 :1@N9_:2@C2 41010 0.785 5.08 0.809 16 :1@C8_:2@C6 40769 0.78 4.6 0.92 17 :1@N9_:2@N9 40768 0.78 5.96 0.498 18 :1@N3_:2@C5 40764 0.78 5.65 0.775 19 :1@N3_:2@O6 40580 0.777 5.27 0.956 20 :1@C8_:2@O6 40353 0.772 4.3 1.11 21 :1@N3_:2@N1 40264 0.77 5.22 0.9 22 :1@C5_:2@O6 39733 0.76 5.03 0.83 23 :1@C4_:2@C4 39500 0.756 5.87 0.547 24 :1@C4_:2@C2 39348 0.753 5.44 0.784 25 :1@C4_:2@N7 39329 0.753 5.84 0.638 26 :1@C5_:2@C6 39276 0.752 5.33 0.73 27 :1@C8_:2@N7 39170 0.75 5.52 0.838 28 :1@C8_:2@N1 38679 0.74 4.68 0.822 29 :1@N7_:2@O6 38677 0.74 4.71 0.955 30 :1@C8_:2@C4 38582 0.738 5.77 0.587 31 :1@N3_:2@C2 38483 0.736 5.53 0.817 32 :1@N3_:2@C4 38441 0.736 5.95 0.618 33 :1@N7_:2@C6 38077 0.729 5.12 0.761 34 :1@C4_:2@N3 37642 0.72 5.91 0.601 35 :1@C5_:2@N1 37409 0.716 5.3 0.831 36 :1@C8_:2@C2 37143 0.711 5.31 0.816 37 :1@N9_:2@N2 36963 0.707 5.42 0.851 38 :1@N3_:2@N3 36603 0.7 5.92 0.629 39 :1@C5_:2@C5 36430 0.697 5.98 0.557 40 :1@N7_:2@N1 36399 0.697 5.13 0.763 41 :1@N7_:2@C5 35953 0.688 5.85 0.594 42 :1@N3_:2@N7 35550 0.68 5.95 0.788 43 :1@C6_:2@O6 35296 0.675 5.64 0.842 44 :1@C2_:2@N1 33463 0.64 5.64 0.901 45 :1@N3_:2@N2 33309 0.637 5.65 0.884 46 :1@C2_:2@C6 33228 0.636 5.71 0.967 47 :1@C6_:2@C6 32736 0.626 5.96 0.704 48 :1@C8_:2@C8 32316 0.618 6.1 0.646 49 :1@C2_:2@O6 32195 0.616 5.52 1.14 50 :1@C8_:2@N9 30782 0.589 6.33 0.492 51 :1@N7_:2@N7 30050 0.575 6.11 0.655 52 :1@C4_:2@C8 29837 0.571 6.27 0.535 53 :1@C4_:2@N9 29369 0.562 6.4 0.442 54 :1@N1_:2@O6 27600 0.528 5.65 1 55 :1@C5_:2@N7 27529 0.527 6.2 0.582 56 :1@N3_:2@N9 26806 0.513 6.38 0.51 57 :1@N6_:2@O6 26123 0.5 6.03 0.758 58 :1@N3_:2@C8 25090 0.48 6.23 0.633 59 :1@N1_:2@C6 25023 0.479 5.91 0.801 60 :1@C2_:2@C5 24210 0.463 5.96 0.814 61 :1@N7_:2@C8 12291 0.235 6.37 0.579 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 52258, 'v_base2' size 52258, output size 52258 TIME: Analyses took 0.0035 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 52258 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 52258 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 52258 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 52258 COM "COM" (double, distance), size is 52258 v_base1 "v_base1" (vector, vector), size is 52258 v_base2 "v_base2" (vector, vector), size is 52258 normalangle "normalangle" (double), size is 52258 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.5488 s ( 99.31%) TIME: Action Post : 0.0002 s ( 0.03%) TIME: Analysis : 0.0035 s ( 0.63%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5526 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: 0.7065 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.