CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 04/19/16 15:32:59 | Available memory: 1.480 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= 105.9407 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 66.2182 100 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C8 38397 0.768 5.04 0.922 2 :1@N9_:2@N7 38333 0.767 4.8 0.926 3 :1@N9_:2@C5 38299 0.766 4.84 0.832 4 :1@N9_:2@N9 38208 0.764 5.27 0.764 5 :1@N9_:2@C4 38016 0.76 5.1 0.755 6 :1@C4_:2@C5 37884 0.758 4.71 0.851 7 :1@C4_:2@C4 37292 0.746 4.9 0.853 8 :1@C4_:2@N7 37226 0.745 4.8 0.937 9 :1@N3_:2@C5 36976 0.74 4.85 0.842 10 :1@C4_:2@C6 36950 0.739 4.79 0.853 11 :1@N9_:2@C6 36602 0.732 5 0.891 12 :1@N3_:2@C4 36595 0.732 4.87 0.893 13 :1@N3_:2@N7 36476 0.73 4.97 0.936 14 :1@C4_:2@C8 36391 0.728 5.02 0.978 15 :1@C4_:2@N9 36289 0.726 5.11 0.906 16 :1@C8_:2@C5 36146 0.723 4.86 0.899 17 :1@C5_:2@C5 36123 0.722 4.72 0.944 18 :1@C5_:2@C6 35962 0.719 4.58 0.909 19 :1@N3_:2@C6 35818 0.716 5.02 0.878 20 :1@N3_:2@N9 35786 0.716 4.98 0.99 21 :1@C4_:2@N6 35687 0.714 5.01 0.913 22 :1@C8_:2@N7 35678 0.714 4.84 1.02 23 :1@N3_:2@C8 35634 0.713 5.01 0.998 24 :1@C8_:2@C4 35570 0.711 5.27 0.811 25 :1@C4_:2@N1 35502 0.71 5.02 0.914 26 :1@C4_:2@N3 35286 0.706 5.12 0.851 27 :1@N9_:2@N3 35279 0.706 5.42 0.819 28 :1@C8_:2@C6 35140 0.703 4.85 0.956 29 :1@C5_:2@N1 35136 0.703 4.76 0.952 30 :1@C5_:2@N6 35124 0.702 4.64 0.936 31 :1@C4_:2@C2 34847 0.697 5.14 0.912 32 :1@N7_:2@C5 34807 0.696 4.83 0.932 33 :1@N7_:2@C6 34790 0.696 4.64 0.954 34 :1@C5_:2@N7 34695 0.694 4.91 0.992 35 :1@C5_:2@C4 34672 0.693 4.99 0.922 36 :1@C2_:2@C5 34650 0.693 4.95 0.915 37 :1@N3_:2@N3 34624 0.692 5.03 0.918 38 :1@N9_:2@N6 34619 0.692 5.17 0.91 39 :1@C8_:2@C8 34578 0.692 5.23 0.927 40 :1@C6_:2@C6 34409 0.688 4.64 0.944 41 :1@C8_:2@N9 34394 0.688 5.54 0.783 42 :1@C2_:2@C6 34090 0.682 4.97 0.914 43 :1@N3_:2@N1 34005 0.68 5.16 0.939 44 :1@N7_:2@N6 33970 0.679 4.54 0.995 45 :1@C6_:2@N6 33937 0.679 4.7 0.976 46 :1@C8_:2@N6 33903 0.678 4.85 1 47 :1@C5_:2@C2 33814 0.676 4.98 0.969 48 :1@C2_:2@C4 33764 0.675 4.88 1.02 49 :1@N3_:2@C2 33712 0.674 5.14 0.936 50 :1@C6_:2@N1 33663 0.673 4.63 0.966 51 :1@N7_:2@N1 33651 0.673 4.89 1.02 52 :1@N7_:2@C4 33640 0.673 5.27 0.865 53 :1@N1_:2@C6 33528 0.671 4.84 0.931 54 :1@C6_:2@C5 33521 0.67 4.87 0.968 55 :1@N3_:2@N6 33517 0.67 5.29 0.991 56 :1@N7_:2@N7 33423 0.668 4.94 1.03 57 :1@N9_:2@N1 33152 0.663 5.24 0.925 58 :1@C2_:2@N1 32952 0.659 4.98 0.953 59 :1@N1_:2@C5 32930 0.659 4.99 0.961 60 :1@C2_:2@N7 32930 0.659 5.18 0.965 61 :1@C5_:2@N3 32882 0.658 5.11 0.922 62 :1@N1_:2@N1 32771 0.655 4.75 0.955 63 :1@N1_:2@N6 32333 0.647 4.98 1.01 64 :1@N9_:2@C2 32318 0.646 5.36 0.913 65 :1@C5_:2@C8 32175 0.643 5.24 0.941 66 :1@C8_:2@N1 32136 0.643 5.09 0.99 67 :1@N6_:2@N6 32070 0.641 4.74 1.04 68 :1@C2_:2@C2 32059 0.641 4.9 0.975 69 :1@C8_:2@N3 31903 0.638 5.52 0.871 70 :1@C5_:2@N9 31857 0.637 5.32 0.897 71 :1@N7_:2@C2 31761 0.635 5.21 1.02 72 :1@N6_:2@C6 31722 0.634 4.79 0.993 73 :1@C2_:2@N3 31698 0.634 4.81 1.02 74 :1@C6_:2@C2 31652 0.633 4.74 0.999 75 :1@C6_:2@N7 31620 0.632 5.21 0.964 76 :1@C2_:2@N6 31600 0.632 5.16 1.04 77 :1@N7_:2@N3 31277 0.626 5.45 0.926 78 :1@C2_:2@C8 31268 0.625 5.22 0.989 79 :1@C6_:2@C4 31225 0.625 4.99 0.983 80 :1@N6_:2@N1 31201 0.624 4.65 1.02 81 :1@C2_:2@N9 31191 0.624 5.01 1.03 82 :1@N1_:2@C2 30927 0.619 4.7 0.995 83 :1@N1_:2@C4 30901 0.618 4.94 1.03 84 :1@N1_:2@N7 30606 0.612 5.34 0.965 85 :1@N7_:2@C8 30341 0.607 5.36 0.898 86 :1@C8_:2@C2 30310 0.606 5.32 0.964 87 :1@N7_:2@N9 30142 0.603 5.6 0.815 88 :1@C6_:2@N3 29954 0.599 4.91 0.996 89 :1@N1_:2@N3 29637 0.593 4.76 1.05 90 :1@N6_:2@C5 29565 0.591 5.18 0.958 91 :1@N6_:2@C2 28840 0.577 4.81 1.07 92 :1@C6_:2@C8 27637 0.553 5.47 0.907 93 :1@N1_:2@N9 27119 0.542 5.21 0.94 94 :1@N1_:2@C8 26994 0.54 5.44 0.928 95 :1@C6_:2@N9 26980 0.54 5.34 0.889 96 :1@N6_:2@C4 26247 0.525 5.28 0.918 97 :1@N6_:2@N7 26106 0.522 5.56 0.923 98 :1@N6_:2@N3 25933 0.519 5.09 0.997 99 :1@N6_:2@N9 20863 0.417 5.7 0.751 100 :1@N6_:2@C8 20095 0.402 5.8 0.791 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 0.0070 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 : 471.9622 s ( 99.93%) TIME: Action Post : 0.3012 s ( 0.06%) TIME: Analysis : 0.0070 s ( 0.00%) TIME: Data File Write : 0.0001 s ( 0.00%) TIME: Other : 0.0006 s ( 0.00%) TIME: Run Total 472.2712 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: 472.8575 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.