CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:13:45 | Available memory: 1.239 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@N1,N2,C2,N3,C4,C5,C6,O6,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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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] [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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, 66 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 34167 of 34167) Coordinate processing will occur on 34167 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*](42) Reference mask: [:1,2&!@H*](42) 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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :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. 6: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c0 (1-34167, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 103 native contacts: Atom ':2@N9' to ':1@N9' Atom ':2@N9' to ':1@C8' Atom ':2@N9' to ':1@N7' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@N3' Atom ':2@N9' to ':1@C4' Atom ':2@C8' to ':1@N9' Atom ':2@C8' to ':1@C8' Atom ':2@C8' to ':1@N7' Atom ':2@C8' to ':1@C5' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@N3' Atom ':2@C8' to ':1@C4' Atom ':2@N7' to ':1@N9' Atom ':2@N7' to ':1@C8' Atom ':2@N7' to ':1@N7' Atom ':2@N7' to ':1@C5' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@N2' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C4' Atom ':2@C5' to ':1@N9' Atom ':2@C5' to ':1@C8' Atom ':2@C5' to ':1@N7' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@O6' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@N2' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C4' Atom ':2@C6' to ':1@N9' Atom ':2@C6' to ':1@C8' Atom ':2@C6' to ':1@N7' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@O6' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@N2' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C4' Atom ':2@N6' to ':1@N9' Atom ':2@N6' to ':1@C8' Atom ':2@N6' to ':1@N7' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@O6' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@N2' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C4' Atom ':2@N1' to ':1@N9' Atom ':2@N1' to ':1@C8' Atom ':2@N1' to ':1@N7' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@O6' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@N2' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C4' Atom ':2@C2' to ':1@N9' Atom ':2@C2' to ':1@C8' Atom ':2@C2' to ':1@N7' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@O6' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@N2' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C4' Atom ':2@N3' to ':1@N9' Atom ':2@N3' to ':1@C8' Atom ':2@N3' to ':1@N7' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@O6' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@N2' Atom ':2@N3' to ':1@N3' Atom ':2@N3' to ':1@C4' Atom ':2@C4' to ':1@N9' Atom ':2@C4' to ':1@C8' Atom ':2@C4' to ':1@N7' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@O6' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@N2' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 34167 frames and processed 34167 frames. TIME: Avg. throughput= 83180.9716 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 97.3171 103 # Contact Nframes Frac. Avg Stdev 1 :2@C4_:1@C4 34133 0.999 4.3 0.53 2 :2@N9_:1@C4 34068 0.997 4.65 0.577 3 :2@C4_:1@N3 34064 0.997 4.4 0.57 4 :2@C5_:1@C4 34055 0.997 4.31 0.656 5 :2@N9_:1@N3 34034 0.996 4.55 0.588 6 :2@C4_:1@N9 33995 0.995 4.67 0.625 7 :2@C4_:1@C5 33965 0.994 4.42 0.633 8 :2@N9_:1@N9 33919 0.993 4.92 0.68 9 :2@C5_:1@N9 33910 0.992 4.41 0.684 10 :2@N3_:1@N3 33901 0.992 4.54 0.621 11 :2@C4_:1@C2 33881 0.992 4.54 0.697 12 :2@N3_:1@C4 33874 0.991 4.49 0.618 13 :2@C5_:1@N3 33861 0.991 4.68 0.696 14 :2@C5_:1@C5 33846 0.991 4.35 0.767 15 :2@C6_:1@C4 33833 0.99 4.52 0.652 16 :2@N3_:1@C2 33781 0.989 4.38 0.687 17 :2@N9_:1@C2 33777 0.989 4.84 0.635 18 :2@N3_:1@C5 33748 0.988 4.37 0.691 19 :2@C4_:1@C6 33731 0.987 4.63 0.632 20 :2@C4_:1@N1 33724 0.987 4.65 0.677 21 :2@N3_:1@C6 33718 0.987 4.28 0.647 22 :2@N3_:1@N1 33715 0.987 4.25 0.646 23 :2@N9_:1@C5 33707 0.987 5.06 0.63 24 :2@N1_:1@C4 33674 0.986 4.7 0.624 25 :2@C8_:1@C4 33652 0.985 4.82 0.762 26 :2@C2_:1@N3 33627 0.984 4.91 0.7 27 :2@C6_:1@N9 33625 0.984 4.65 0.642 28 :2@C6_:1@C5 33624 0.984 4.2 0.775 29 :2@N1_:1@C5 33621 0.984 4.17 0.687 30 :2@C2_:1@C5 33619 0.984 4.21 0.691 31 :2@C2_:1@C4 33614 0.984 4.63 0.656 32 :2@C2_:1@C6 33612 0.984 4.02 0.696 33 :2@C8_:1@N3 33518 0.981 4.89 0.723 34 :2@C2_:1@C2 33492 0.98 4.68 0.792 35 :2@N7_:1@C4 33482 0.98 4.64 0.828 36 :2@C2_:1@N1 33476 0.98 4.26 0.769 37 :2@N9_:1@N1 33465 0.979 5.23 0.581 38 :2@C6_:1@N3 33460 0.979 5.07 0.753 39 :2@N1_:1@N3 33438 0.979 5.21 0.749 40 :2@C5_:1@N7 33432 0.978 4.49 0.862 41 :2@C4_:1@N7 33408 0.978 4.84 0.776 42 :2@C5_:1@C8 33382 0.977 4.47 0.844 43 :2@N1_:1@C6 33345 0.976 4.16 0.817 44 :2@C4_:1@C8 33330 0.976 4.92 0.772 45 :2@C6_:1@N7 33329 0.975 4.15 0.87 46 :2@N9_:1@C6 33319 0.975 5.38 0.576 47 :2@C2_:1@O6 33270 0.974 4.17 0.803 48 :2@N3_:1@O6 33239 0.973 4.67 0.73 49 :2@N7_:1@N3 33204 0.972 4.97 0.79 50 :2@N1_:1@N7 33159 0.97 4.25 0.824 51 :2@C4_:1@N2 33132 0.97 5.08 0.863 52 :2@N3_:1@N2 33123 0.969 4.85 0.88 53 :2@C6_:1@C8 33121 0.969 4.38 0.81 54 :2@N3_:1@N9 33110 0.969 5.06 0.733 55 :2@C8_:1@N9 33043 0.967 4.74 0.812 56 :2@C5_:1@C2 32995 0.966 4.95 0.84 57 :2@N7_:1@N9 32989 0.966 4.44 0.834 58 :2@N1_:1@N9 32885 0.962 5.03 0.668 59 :2@N6_:1@C4 32868 0.962 5.02 0.744 60 :2@C2_:1@N7 32828 0.961 4.56 0.877 61 :2@C4_:1@O6 32825 0.961 5.19 0.659 62 :2@C5_:1@C6 32742 0.958 4.73 0.765 63 :2@N6_:1@N9 32736 0.958 4.95 0.693 64 :2@C8_:1@C2 32584 0.954 5.39 0.743 65 :2@N3_:1@N7 32579 0.954 4.88 0.839 66 :2@N1_:1@O6 32551 0.953 4.2 0.851 67 :2@C6_:1@C6 32502 0.951 4.44 0.84 68 :2@N1_:1@N1 32487 0.951 4.58 0.906 69 :2@C8_:1@C5 32482 0.951 5.28 0.735 70 :2@N1_:1@C8 32453 0.95 4.71 0.807 71 :2@C2_:1@N9 32361 0.947 5.14 0.772 72 :2@N6_:1@N7 32360 0.947 4.21 0.96 73 :2@N9_:1@C8 32352 0.947 5.37 0.76 74 :2@N1_:1@C2 32343 0.947 5.05 0.898 75 :2@N6_:1@C5 32242 0.944 4.55 0.844 76 :2@N7_:1@C8 32227 0.943 4.62 0.95 77 :2@N6_:1@C8 32220 0.943 4.4 0.85 78 :2@N7_:1@C5 32189 0.942 4.88 0.818 79 :2@N9_:1@N7 32034 0.938 5.49 0.739 80 :2@C5_:1@N1 31963 0.935 4.94 0.809 81 :2@C8_:1@C8 31835 0.932 5.17 0.862 82 :2@C2_:1@C8 31681 0.927 5.02 0.881 83 :2@N3_:1@C8 31655 0.926 5.17 0.813 84 :2@C6_:1@C2 31449 0.92 5.12 0.901 85 :2@N7_:1@N7 31368 0.918 4.9 0.888 86 :2@C2_:1@N2 31316 0.917 5.21 0.917 87 :2@C6_:1@N1 31195 0.913 4.84 0.899 88 :2@C6_:1@O6 30974 0.907 4.64 0.779 89 :2@N7_:1@C2 30627 0.896 5.39 0.804 90 :2@C5_:1@O6 30566 0.895 5.17 0.668 91 :2@C8_:1@N7 30287 0.886 5.45 0.767 92 :2@N6_:1@C6 30183 0.883 4.82 0.857 93 :2@N7_:1@C6 29860 0.874 5.4 0.708 94 :2@N6_:1@N3 29762 0.871 5.61 0.779 95 :2@N6_:1@O6 29228 0.855 4.94 0.885 96 :2@N7_:1@N1 29144 0.853 5.59 0.775 97 :2@C5_:1@N2 28991 0.849 5.48 0.871 98 :2@N6_:1@N1 27640 0.809 5.34 0.948 99 :2@N1_:1@N2 25950 0.76 5.48 0.913 100 :2@N6_:1@C2 25420 0.744 5.56 0.899 101 :2@N7_:1@N2 24856 0.727 5.82 0.828 102 :2@C6_:1@N2 24509 0.717 5.56 0.913 103 :2@N6_:1@N2 15554 0.455 5.74 1.05 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 34167, 'v_base2' size 34167, output size 34167 TIME: Analyses took 0.0044 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 34167 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 34167 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 34167 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 34167 COM "COM" (double, distance), size is 34167 v_base1 "v_base1" (vector, vector), size is 34167 v_base2 "v_base2" (vector, vector), size is 34167 normalangle "normalangle" (double), size is 34167 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.4108 s ( 98.86%) TIME: Action Post : 0.0003 s ( 0.07%) TIME: Analysis : 0.0044 s ( 1.05%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.4155 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: 0.6218 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.