CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 04/23/16 13:30:11 | Available memory: 1.402 GB 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 100 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@N1' Atom ':1@N9' to ':2@C2' 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@N6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N3' 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@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N3' 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@N3' 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= 100.3066 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 62.5966 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 36960 0.739 4.89 0.821 2 :1@N9_:2@N7 36668 0.733 4.91 0.945 3 :1@C4_:2@C5 36638 0.733 4.8 0.85 4 :1@N9_:2@C4 36598 0.732 5.16 0.737 5 :1@N9_:2@C8 36383 0.728 5.19 0.93 6 :1@N3_:2@C5 36315 0.726 4.96 0.855 7 :1@N9_:2@N9 36301 0.726 5.4 0.758 8 :1@C4_:2@C6 36020 0.72 4.83 0.824 9 :1@C4_:2@C4 35906 0.718 5 0.853 10 :1@N3_:2@C4 35803 0.716 5.01 0.901 11 :1@C4_:2@N7 35759 0.715 4.94 0.97 12 :1@N9_:2@C6 35720 0.714 4.98 0.868 13 :1@N3_:2@C6 35395 0.708 5.07 0.883 14 :1@N3_:2@N7 35381 0.708 5.08 0.952 15 :1@C4_:2@N6 34902 0.698 5.02 0.886 16 :1@C4_:2@N1 34863 0.697 5.01 0.88 17 :1@C5_:2@C6 34784 0.696 4.67 0.925 18 :1@C4_:2@C8 34426 0.689 5.18 1 19 :1@C8_:2@C5 34399 0.688 4.94 0.924 20 :1@C5_:2@C5 34390 0.688 4.85 0.98 21 :1@C4_:2@N9 34364 0.687 5.27 0.915 22 :1@C4_:2@N3 34292 0.686 5.19 0.875 23 :1@N9_:2@N3 34270 0.685 5.42 0.808 24 :1@N3_:2@N9 34230 0.685 5.14 0.99 25 :1@N3_:2@C8 34188 0.684 5.15 1.01 26 :1@C5_:2@N1 34094 0.682 4.79 0.948 27 :1@C5_:2@N6 34054 0.681 4.71 0.944 28 :1@C4_:2@C2 34046 0.681 5.14 0.912 29 :1@N9_:2@N6 33997 0.68 5.13 0.904 30 :1@N3_:2@N3 33904 0.678 5.14 0.928 31 :1@C8_:2@C6 33885 0.678 4.85 0.975 32 :1@N3_:2@N1 33813 0.676 5.19 0.94 33 :1@C8_:2@C4 33543 0.671 5.34 0.815 34 :1@N3_:2@C2 33360 0.667 5.2 0.94 35 :1@N7_:2@C6 33325 0.666 4.7 0.983 36 :1@C8_:2@N7 33155 0.663 4.95 1.04 37 :1@C2_:2@C5 33097 0.662 5.04 0.927 38 :1@N3_:2@N6 33056 0.661 5.3 0.992 39 :1@C2_:2@C6 32980 0.66 5.04 0.942 40 :1@N9_:2@N1 32959 0.659 5.17 0.899 41 :1@C6_:2@C6 32953 0.659 4.76 0.988 42 :1@C8_:2@N6 32705 0.654 4.82 1.04 43 :1@N7_:2@C5 32680 0.654 4.93 0.968 44 :1@N7_:2@N6 32648 0.653 4.59 1.03 45 :1@N7_:2@N1 32551 0.651 4.88 1.03 46 :1@C6_:2@N6 32546 0.651 4.8 1 47 :1@C5_:2@C2 32540 0.651 5.01 1 48 :1@C5_:2@C4 32504 0.65 5.09 0.957 49 :1@C6_:2@N1 32297 0.646 4.73 0.992 50 :1@C5_:2@N7 32243 0.645 5.04 1.03 51 :1@N9_:2@C2 32076 0.642 5.3 0.9 52 :1@C2_:2@N1 32000 0.64 5.06 0.979 53 :1@N1_:2@C6 31727 0.635 4.92 0.944 54 :1@C2_:2@C4 31661 0.633 4.98 1.01 55 :1@C8_:2@N1 31631 0.633 5.04 0.998 56 :1@C8_:2@C8 31310 0.626 5.35 0.94 57 :1@C8_:2@N9 31273 0.625 5.64 0.788 58 :1@C2_:2@N7 31265 0.625 5.26 0.978 59 :1@C6_:2@C5 31259 0.625 4.99 1 60 :1@N1_:2@N1 31249 0.625 4.86 0.967 61 :1@N7_:2@C4 31015 0.62 5.34 0.891 62 :1@C5_:2@N3 30874 0.617 5.17 0.966 63 :1@C2_:2@C2 30786 0.616 5 0.978 64 :1@N1_:2@C5 30712 0.614 5.08 0.973 65 :1@C8_:2@N3 30637 0.613 5.52 0.864 66 :1@N1_:2@N6 30620 0.612 5.02 1.03 67 :1@N7_:2@N7 30551 0.611 5.06 1.06 68 :1@C2_:2@N6 30504 0.61 5.18 1.07 69 :1@N7_:2@C2 30481 0.61 5.2 1.03 70 :1@N6_:2@N6 30083 0.602 4.85 1.07 71 :1@C8_:2@C2 29993 0.6 5.29 0.968 72 :1@C2_:2@N3 29838 0.597 4.93 1.03 73 :1@C6_:2@C2 29699 0.594 4.81 1.03 74 :1@N6_:2@C6 29412 0.588 4.9 1.04 75 :1@N6_:2@N1 29263 0.585 4.76 1.07 76 :1@N1_:2@C2 29149 0.583 4.81 1.01 77 :1@N7_:2@N3 29095 0.582 5.47 0.936 78 :1@C2_:2@C8 29054 0.581 5.31 1 79 :1@C2_:2@N9 28766 0.575 5.12 1.03 80 :1@C5_:2@C8 28687 0.574 5.33 0.949 81 :1@C6_:2@N7 28448 0.569 5.28 0.973 82 :1@N1_:2@C4 28415 0.568 5.03 1.04 83 :1@C6_:2@C4 28373 0.567 5.06 1 84 :1@C5_:2@N9 28305 0.566 5.4 0.893 85 :1@N1_:2@N7 27963 0.559 5.39 0.977 86 :1@C6_:2@N3 27245 0.545 4.95 1.02 87 :1@N1_:2@N3 27147 0.543 4.85 1.06 88 :1@N6_:2@C5 26294 0.526 5.23 0.969 89 :1@N7_:2@C8 26270 0.525 5.43 0.9 90 :1@N6_:2@C2 26263 0.525 4.84 1.08 91 :1@N7_:2@N9 26131 0.523 5.66 0.813 92 :1@C6_:2@C8 24183 0.484 5.51 0.893 93 :1@N1_:2@N9 24091 0.482 5.25 0.931 94 :1@N1_:2@C8 23998 0.48 5.48 0.925 95 :1@C6_:2@N9 23651 0.473 5.38 0.866 96 :1@N6_:2@N3 23006 0.46 5.09 0.99 97 :1@N6_:2@C4 23002 0.46 5.29 0.908 98 :1@N6_:2@N7 22694 0.454 5.58 0.908 99 :1@N6_:2@N9 18363 0.367 5.74 0.729 100 :1@N6_:2@C8 17429 0.349 5.84 0.766 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 0.0061 seconds. DATASETS (8 total): 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 : 0.0001 s ( 0.00%) TIME: Trajectory Process : 498.4715 s ( 99.95%) TIME: Action Post : 0.2609 s ( 0.05%) TIME: Analysis : 0.0061 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 498.7388 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: 499.3634 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.