CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 12:06:56 | Available memory: 1.223 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.c3] Reading '../ctraj.c3' 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,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':1@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 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] DISTANCE: :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2, center of mass. [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@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.c3' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 8203 of 8203) Coordinate processing will occur on 8203 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 :2@N1,C6,C5,C4,N4,N3,C2,O2 :1@N1,C6,C5,C4,O4,N3,C2,O2 mindist] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2] :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2 (11 atoms), imaged. 5: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :1@N1,C6,C5,C4,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c3 (1-8203, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. Setup 64 native contacts: Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@O4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@O4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@O4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C4' Atom ':2@C4' to ':1@O4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' Atom ':2@N4' to ':1@N1' Atom ':2@N4' to ':1@C6' Atom ':2@N4' to ':1@C5' Atom ':2@N4' to ':1@C4' Atom ':2@N4' to ':1@O4' Atom ':2@N4' to ':1@N3' Atom ':2@N4' to ':1@C2' Atom ':2@N4' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@O4' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@O4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@O2' to ':1@N1' Atom ':2@O2' to ':1@C6' Atom ':2@O2' to ':1@C5' Atom ':2@O2' to ':1@C4' Atom ':2@O2' to ':1@O4' Atom ':2@O2' to ':1@N3' Atom ':2@O2' to ':1@C2' Atom ':2@O2' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 8203 frames and processed 8203 frames. TIME: Avg. throughput= 74252.0932 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 50.0469 64 # Contact Nframes Frac. Avg Stdev 1 :2@C6_:1@N1 7428 0.906 4.93 0.83 2 :2@C6_:1@C2 7145 0.871 4.93 0.932 3 :2@C6_:1@C6 7078 0.863 5.02 0.873 4 :2@C5_:1@C2 7074 0.862 4.51 0.946 5 :2@N1_:1@N1 7069 0.862 5.26 0.721 6 :2@C5_:1@N1 7036 0.858 4.56 0.788 7 :2@C5_:1@O2 6986 0.852 4.66 0.995 8 :2@N1_:1@C6 6964 0.849 5.19 0.862 9 :2@C5_:1@C6 6812 0.83 4.75 0.846 10 :2@C6_:1@O2 6764 0.825 4.96 1.01 11 :2@C4_:1@C2 6750 0.823 4.41 0.898 12 :2@C5_:1@N3 6730 0.82 4.65 0.918 13 :2@N1_:1@C5 6726 0.82 5.19 0.945 14 :2@C4_:1@N1 6725 0.82 4.67 0.732 15 :2@C6_:1@C5 6687 0.815 5.21 0.862 16 :2@N4_:1@C2 6656 0.811 4.5 0.828 17 :2@C4_:1@N3 6642 0.81 4.24 0.97 18 :2@C2_:1@C5 6621 0.807 4.94 0.995 19 :2@C4_:1@O2 6609 0.806 4.64 0.954 20 :2@N4_:1@N3 6607 0.805 4.22 0.919 21 :2@N1_:1@C2 6582 0.802 5.1 0.857 22 :2@N4_:1@N1 6568 0.801 4.87 0.719 23 :2@C2_:1@C6 6544 0.798 5.17 0.835 24 :2@C6_:1@N3 6528 0.796 5.07 0.807 25 :2@C4_:1@C6 6521 0.795 4.71 0.801 26 :2@N4_:1@O2 6507 0.793 4.71 0.966 27 :2@C5_:1@C5 6491 0.791 4.87 0.819 28 :2@C2_:1@N1 6477 0.79 5.28 0.689 29 :2@C5_:1@C4 6470 0.789 4.87 0.803 30 :2@C4_:1@C4 6462 0.788 4.33 0.846 31 :2@N3_:1@N1 6461 0.788 5.03 0.722 32 :2@N3_:1@C2 6446 0.786 4.68 0.919 33 :2@N4_:1@C4 6426 0.783 4.31 0.865 34 :2@N3_:1@C4 6418 0.782 4.3 0.945 35 :2@C2_:1@C4 6417 0.782 4.76 0.937 36 :2@N3_:1@N3 6411 0.782 4.3 1.02 37 :2@C6_:1@C4 6409 0.781 5.3 0.742 38 :2@N1_:1@C4 6407 0.781 5.23 0.786 39 :2@C4_:1@C5 6392 0.779 4.53 0.817 40 :2@N3_:1@C5 6381 0.778 4.58 0.865 41 :2@N3_:1@C6 6364 0.776 4.93 0.776 42 :2@N4_:1@C6 6325 0.771 4.88 0.888 43 :2@C2_:1@C2 6314 0.77 5 0.905 44 :2@C2_:1@N3 6269 0.764 4.73 0.957 45 :2@N1_:1@N3 6265 0.764 5.08 0.797 46 :2@N4_:1@O4 6259 0.763 4.51 0.891 47 :2@N4_:1@C5 6251 0.762 4.6 0.93 48 :2@C4_:1@O4 6235 0.76 4.64 0.817 49 :2@N3_:1@O4 6215 0.758 4.4 0.925 50 :2@O2_:1@C5 6158 0.751 5.21 1.02 51 :2@N3_:1@O2 6157 0.751 4.94 0.951 52 :2@N1_:1@O2 6138 0.748 5.16 1.08 53 :2@C2_:1@O4 6107 0.744 4.9 0.902 54 :2@O2_:1@C4 6046 0.737 5 0.928 55 :2@C5_:1@O4 5990 0.73 5.36 0.723 56 :2@C2_:1@O2 5942 0.724 5.18 1.06 57 :2@O2_:1@N3 5847 0.713 5.08 0.939 58 :2@O2_:1@C6 5843 0.712 5.58 0.812 59 :2@O2_:1@O4 5838 0.712 4.94 0.95 60 :2@N1_:1@O4 5838 0.712 5.55 0.719 61 :2@O2_:1@N1 5697 0.695 5.82 0.649 62 :2@C6_:1@O4 5687 0.693 5.78 0.649 63 :2@O2_:1@C2 5632 0.687 5.47 0.855 64 :2@O2_:1@O2 4691 0.572 5.47 1.03 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 8203, 'v_base2' size 8203, output size 8203 TIME: Analyses took 0.0011 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 8203 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 8203 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 8203 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 8203 COM "COM" (double, distance), size is 8203 v_base1 "v_base1" (vector, vector), size is 8203 v_base2 "v_base2" (vector, vector), size is 8203 normalangle "normalangle" (double), size is 8203 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.03%) TIME: Trajectory Process : 0.1105 s ( 98.76%) TIME: Action Post : 0.0002 s ( 0.19%) TIME: Analysis : 0.0011 s ( 0.97%) TIME: Data File Write : 0.0000 s ( 0.02%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1119 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: 0.1588 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.