CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/16/16 15:53:24 | Available memory: 822.051 MB INPUT: Reading input from 'pt-criteria.in' [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [strip :WAT,Na+,K+,Cl-] Warning: Action specified before trajin/ensemble. Assuming trajin. STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [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,C2,N3,C4,C5,C6,N6,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,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9] 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,N6,H61,H62,N7,C8,H8,N9, 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,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [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. [trajin ../../traj.1.01 remdtraj remdtrajtemp 396.40 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] Reading '../../traj.1.01' as Amber NetCDF [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [traj] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (1 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 K Coordinate processing will occur on 50000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (7 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](41) Reference mask: [:1,2&!@H*](41) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,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,N6,H61,H62,N7,C8,H8,N9] :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,N6,H61,H62,N7,C8,H8,N9 (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,N6,N7,C8,N9 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- traj.1.01 (1-50000, 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,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 90 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@N6' 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@N6' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@N9' 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@N6' Atom ':1@N7' to ':2@C4' Atom ':1@C5' to ':2@N9' Atom ':1@C5' to ':2@C8' Atom ':1@C5' to ':2@N7' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@N6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@N9' Atom ':1@C6' to ':2@C8' Atom ':1@C6' to ':2@N7' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@N6' to ':2@N9' Atom ':1@N6' to ':2@C8' Atom ':1@N6' to ':2@N7' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@C4' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' 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@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' 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@N6' 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 50000 frames and processed 50000 frames. TIME: Avg. throughput= 816.6452 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 56.1933 90 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N7 37053 0.741 4.9 0.934 2 :1@N9_:2@C5 36905 0.738 4.97 0.807 3 :1@N9_:2@C8 36862 0.737 5.12 0.966 4 :1@C4_:2@C5 36456 0.729 4.8 0.866 5 :1@N9_:2@C4 36394 0.728 5.24 0.738 6 :1@N3_:2@C5 36329 0.727 4.93 0.865 7 :1@N9_:2@N9 36085 0.722 5.38 0.79 8 :1@C4_:2@C6 35810 0.716 4.92 0.801 9 :1@C4_:2@N7 35805 0.716 4.85 1.01 10 :1@N3_:2@C4 35692 0.714 4.95 0.936 11 :1@N3_:2@N7 35555 0.711 4.98 0.975 12 :1@C4_:2@C4 35554 0.711 4.99 0.876 13 :1@N3_:2@C6 35413 0.708 5.14 0.84 14 :1@N9_:2@C6 35291 0.706 5.13 0.889 15 :1@C4_:2@N1 34651 0.693 5.19 0.861 16 :1@C4_:2@N6 34649 0.693 5.12 0.863 17 :1@C5_:2@C6 34407 0.688 4.72 0.922 18 :1@N3_:2@C8 34400 0.688 4.98 1.08 19 :1@C4_:2@C8 34316 0.686 5.02 1.08 20 :1@C8_:2@C5 34120 0.682 5.03 0.905 21 :1@C4_:2@N3 34074 0.681 5.28 0.848 22 :1@N3_:2@N9 34069 0.681 4.97 1.06 23 :1@N3_:2@N3 33983 0.68 5.15 0.918 24 :1@C4_:2@C2 33960 0.679 5.31 0.878 25 :1@C5_:2@C5 33950 0.679 4.79 1.03 26 :1@C5_:2@N1 33773 0.675 4.95 0.921 27 :1@N3_:2@N1 33769 0.675 5.32 0.892 28 :1@C5_:2@N6 33664 0.673 4.75 0.901 29 :1@C4_:2@N9 33546 0.671 5.12 0.975 30 :1@N3_:2@C2 33475 0.669 5.31 0.903 31 :1@C8_:2@N7 33411 0.668 4.95 1.03 32 :1@C8_:2@C6 33409 0.668 5.02 0.977 33 :1@N9_:2@N6 33270 0.665 5.26 0.938 34 :1@N3_:2@N6 33167 0.663 5.41 0.95 35 :1@C2_:2@C6 33048 0.661 5.05 0.912 36 :1@C8_:2@C4 32924 0.658 5.45 0.816 37 :1@C2_:2@C5 32923 0.658 4.93 0.971 38 :1@N7_:2@C6 32828 0.657 4.8 0.969 39 :1@C6_:2@C6 32500 0.65 4.7 1.02 40 :1@N7_:2@N6 32446 0.649 4.69 0.998 41 :1@C8_:2@N6 32403 0.648 4.98 1.04 42 :1@C6_:2@N6 32320 0.646 4.77 0.984 43 :1@C5_:2@C2 32258 0.645 5.18 0.963 44 :1@N7_:2@C5 32107 0.642 4.94 0.978 45 :1@C2_:2@N1 32097 0.642 5.11 0.938 46 :1@C6_:2@N1 32075 0.641 4.77 0.995 47 :1@C5_:2@N7 31850 0.637 4.88 1.1 48 :1@C5_:2@C4 31663 0.633 5.03 0.975 49 :1@N1_:2@C6 31531 0.631 4.85 0.973 50 :1@C2_:2@C4 31509 0.63 4.83 1.07 51 :1@C8_:2@C8 31367 0.627 5.29 0.956 52 :1@C2_:2@N7 31178 0.624 5.09 1 53 :1@N1_:2@N1 31131 0.623 4.84 0.983 54 :1@C2_:2@N6 30970 0.619 5.27 0.998 55 :1@C2_:2@C2 30872 0.617 5.01 0.986 56 :1@N1_:2@N6 30845 0.617 5.03 0.986 57 :1@C6_:2@C5 30432 0.609 4.8 1.07 58 :1@C8_:2@N9 30422 0.608 5.63 0.783 59 :1@N7_:2@N7 30414 0.608 4.96 1.09 60 :1@C5_:2@N3 30268 0.605 5.23 0.928 61 :1@N1_:2@C5 30197 0.604 4.89 1.04 62 :1@N7_:2@C4 30008 0.6 5.36 0.891 63 :1@C2_:2@N3 29890 0.598 4.83 1.05 64 :1@N6_:2@N6 29784 0.596 4.72 1.1 65 :1@C6_:2@C2 29544 0.591 4.86 1.02 66 :1@C2_:2@C8 29145 0.583 5.08 1.04 67 :1@N1_:2@C2 29012 0.58 4.76 1.04 68 :1@N6_:2@N1 28756 0.575 4.7 1.09 69 :1@N6_:2@C6 28739 0.575 4.73 1.09 70 :1@C2_:2@N9 28662 0.573 4.86 1.06 71 :1@C5_:2@C8 28157 0.563 5.1 1.01 72 :1@N1_:2@C4 27999 0.56 4.79 1.06 73 :1@C6_:2@N7 27962 0.559 5.02 1.05 74 :1@N1_:2@N7 27933 0.559 5.16 1.03 75 :1@C6_:2@C4 27615 0.552 4.87 0.993 76 :1@C5_:2@N9 27278 0.546 5.19 0.893 77 :1@N1_:2@N3 27124 0.542 4.71 1.06 78 :1@C6_:2@N3 26914 0.538 4.9 0.971 79 :1@N7_:2@C8 26037 0.521 5.27 0.924 80 :1@N6_:2@C2 25863 0.517 4.81 1.05 81 :1@N6_:2@C5 25632 0.513 4.96 0.997 82 :1@N7_:2@N9 25324 0.506 5.56 0.799 83 :1@N1_:2@N9 24919 0.498 5.02 0.933 84 :1@N1_:2@C8 24570 0.491 5.22 0.943 85 :1@C6_:2@C8 24438 0.489 5.23 0.929 86 :1@C6_:2@N9 24255 0.485 5.17 0.858 87 :1@N6_:2@C4 23525 0.47 5.13 0.884 88 :1@N6_:2@N7 22997 0.46 5.3 0.949 89 :1@N6_:2@N9 20263 0.405 5.63 0.734 90 :1@N6_:2@C8 19475 0.39 5.65 0.774 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 50000, 'v_base2' size 50000, output size 50000 TIME: Analyses took 0.0037 seconds. DATASETS (9 total): [traj] "[traj]" (topology), size is 3301 full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent RMSD_00001 "RMSD_00001" (double, rms), size is 50000 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 50000 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 50000 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 50000 COM "COM" (double, distance), size is 50000 v_base1 "v_base1" (vector, vector), size is 50000 v_base2 "v_base2" (vector, vector), size is 50000 normalangle "normalangle" (double), size is 50000 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 61.2261 s ( 99.98%) TIME: Action Post : 0.0038 s ( 0.01%) TIME: Analysis : 0.0037 s ( 0.01%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0074 s ( 0.00%) TIME: Run Total 61.2412 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw_396.40.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw_396.40.dat, format 'Standard Data File' Warning: 'Contacts_00001[mindist]' selects no data sets. Warning: Contacts_00001[mindist] does not correspond to any data sets. COM normalangle TIME: Total execution time: 61.4106 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.