CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 11:49:15 | Available memory: 1.221 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.c0] Reading '../ctraj.c0' 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,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' 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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [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] [vector v_base2 :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, 60 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 55868 of 55868) Coordinate processing will occur on 55868 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*](37) Reference mask: [:1,2&!@H*](37) 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,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [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. 6: [vector v_base2 :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.c0 (1-55868, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 64 native contacts: 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@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@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@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' Atom ':1@N4' to ':2@N1' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@C5' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@O4' Atom ':1@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' 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@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@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 55868 frames and processed 55868 frames. TIME: Avg. throughput= 100833.1168 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 61.5589 64 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 55631 0.996 4.21 0.518 2 :1@N1_:2@C5 55569 0.995 4.39 0.523 3 :1@N1_:2@N1 55224 0.988 4.52 0.463 4 :1@N1_:2@C4 55188 0.988 4.9 0.501 5 :1@C6_:2@C5 55135 0.987 3.89 0.527 6 :1@C2_:2@C6 55114 0.987 4.41 0.628 7 :1@C6_:2@C6 55031 0.985 4.1 0.529 8 :1@C2_:2@C5 55016 0.985 4.75 0.637 9 :1@C6_:2@C4 54936 0.983 4.25 0.514 10 :1@N1_:2@N3 54822 0.981 5.12 0.492 11 :1@N1_:2@C2 54780 0.981 4.98 0.462 12 :1@C2_:2@N1 54771 0.98 4.32 0.59 13 :1@C6_:2@O4 54730 0.98 4.66 0.56 14 :1@C6_:2@N3 54681 0.979 4.71 0.553 15 :1@C6_:2@N1 54658 0.978 4.61 0.531 16 :1@C2_:2@C4 54585 0.977 5.03 0.632 17 :1@C5_:2@C4 54563 0.977 3.71 0.51 18 :1@O2_:2@C6 54550 0.976 4.97 0.686 19 :1@C5_:2@C5 54531 0.976 3.78 0.528 20 :1@C6_:2@C2 54515 0.976 4.91 0.565 21 :1@C2_:2@C2 54507 0.976 4.6 0.582 22 :1@C2_:2@N3 54478 0.975 4.92 0.621 23 :1@C5_:2@O4 54475 0.975 3.95 0.567 24 :1@C5_:2@N3 54422 0.974 4.04 0.581 25 :1@N1_:2@O4 54411 0.974 5.52 0.537 26 :1@O2_:2@N1 54375 0.973 4.72 0.699 27 :1@N3_:2@N3 54285 0.972 4.28 0.666 28 :1@C4_:2@C4 54278 0.972 3.92 0.58 29 :1@C4_:2@N3 54255 0.971 3.82 0.533 30 :1@N3_:2@C5 54238 0.971 4.65 0.675 31 :1@N3_:2@C4 54222 0.971 4.58 0.702 32 :1@C5_:2@C6 54181 0.97 4.2 0.518 33 :1@C5_:2@C2 54178 0.97 4.45 0.651 34 :1@C4_:2@O4 54153 0.969 4.31 0.692 35 :1@N3_:2@C2 54131 0.969 4.11 0.607 36 :1@C4_:2@C5 54112 0.969 4.2 0.582 37 :1@N3_:2@C6 54063 0.968 4.49 0.607 38 :1@C4_:2@C2 54028 0.967 4.03 0.563 39 :1@C5_:2@N1 54012 0.967 4.51 0.595 40 :1@N3_:2@N1 53969 0.966 4.21 0.584 41 :1@N4_:2@N3 53882 0.964 3.74 0.571 42 :1@C4_:2@C6 53854 0.964 4.39 0.515 43 :1@N4_:2@C4 53823 0.963 4.04 0.632 44 :1@C4_:2@N1 53798 0.963 4.3 0.543 45 :1@C2_:2@O2 53784 0.963 5.02 0.594 46 :1@O2_:2@C2 53748 0.962 5.09 0.718 47 :1@N3_:2@O2 53736 0.962 4.39 0.639 48 :1@N4_:2@O4 53679 0.961 4.23 0.787 49 :1@N4_:2@C2 53631 0.96 4.12 0.632 50 :1@C4_:2@O2 53628 0.96 4.47 0.678 51 :1@N4_:2@C5 53518 0.958 4.69 0.608 52 :1@N1_:2@O2 53489 0.957 5.65 0.501 53 :1@N4_:2@N1 53375 0.955 4.76 0.601 54 :1@N4_:2@C6 53331 0.955 5.02 0.538 55 :1@O2_:2@C5 53222 0.953 5.51 0.669 56 :1@N4_:2@O2 53202 0.952 4.35 0.787 57 :1@C5_:2@O2 53112 0.951 5.15 0.736 58 :1@N3_:2@O4 53083 0.95 5.15 0.739 59 :1@O2_:2@O2 52531 0.94 5.33 0.726 60 :1@C6_:2@O2 52492 0.94 5.68 0.604 61 :1@C2_:2@O4 52023 0.931 5.68 0.618 62 :1@O2_:2@N3 51765 0.927 5.59 0.699 63 :1@O2_:2@C4 49990 0.895 5.8 0.654 64 :1@O2_:2@O4 33671 0.603 6.27 0.58 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 55868, 'v_base2' size 55868, output size 55868 TIME: Analyses took 0.0042 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 55868 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 55868 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 55868 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 55868 COM "COM" (double, distance), size is 55868 v_base1 "v_base1" (vector, vector), size is 55868 v_base2 "v_base2" (vector, vector), size is 55868 normalangle "normalangle" (double), size is 55868 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.5541 s ( 99.21%) TIME: Action Post : 0.0001 s ( 0.02%) TIME: Analysis : 0.0042 s ( 0.75%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5585 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: 0.7101 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.