CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 12/03/15 15:34:35 | Available memory: 53202.9 MB INPUT: Reading Input from file 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-] 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*), with fitting. [nativecontacts :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@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_00001 Saving minimum observed distances in set 'Contacts_00001[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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :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] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@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: 0: [traj] 'noWAt.topo.hmr', 67 atoms, 2 res, box: Orthogonal, 1 mol, 202425 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 202425 of 202425) Coordinate processing will occur on 202425 frames. TIME: Run Initialization took 0.0007 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. ----- ctraj.c0 (1-202425, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 118 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@O6' 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@O6' 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@O6' 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@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' 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@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C4' Atom ':1@O6' to ':2@N9' Atom ':1@O6' to ':2@C8' Atom ':1@O6' to ':2@N7' Atom ':1@O6' to ':2@C5' Atom ':1@O6' to ':2@C6' Atom ':1@O6' to ':2@O6' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@C2' Atom ':1@O6' to ':2@N2' Atom ':1@O6' to ':2@N3' Atom ':1@O6' 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@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' 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@O6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N9' Atom ':1@N2' to ':2@C8' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' 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@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' 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@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 202425 frames and processed 202425 frames. TIME: Trajectory processing: 1.3588 s TIME: Avg. throughput= 148970.8373 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 111.742 118 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 202136 0.999 4.69 0.815 2 :1@C4_:2@C5 202117 0.998 4.23 0.433 3 :1@C4_:2@C4 202074 0.998 4.45 0.5 4 :1@N9_:2@N9 202035 0.998 4.94 0.534 5 :1@C4_:2@N7 201991 0.998 4.35 0.651 6 :1@N3_:2@C4 201749 0.997 4.4 0.535 7 :1@N9_:2@C5 201669 0.996 4.65 0.539 8 :1@C5_:2@C5 201559 0.996 4.17 0.615 9 :1@N3_:2@C5 201496 0.995 4.44 0.511 10 :1@N9_:2@N7 201396 0.995 4.52 0.656 11 :1@C6_:2@C5 201371 0.995 4.33 0.835 12 :1@C4_:2@C8 201318 0.995 4.57 0.913 13 :1@C4_:2@C6 201260 0.994 4.48 0.71 14 :1@N3_:2@N9 201117 0.994 4.56 0.928 15 :1@N9_:2@C4 201093 0.993 4.89 0.518 16 :1@C6_:2@C6 201011 0.993 3.99 0.52 17 :1@N3_:2@N3 200999 0.993 4.72 0.562 18 :1@N1_:2@C6 200904 0.992 4.26 0.587 19 :1@C5_:2@C4 200900 0.992 4.65 0.75 20 :1@C5_:2@C6 200828 0.992 4.1 0.517 21 :1@N1_:2@C5 200793 0.992 4.47 0.784 22 :1@N9_:2@C8 200734 0.992 4.65 0.765 23 :1@C6_:2@O6 200686 0.991 4.02 0.656 24 :1@N3_:2@N7 200624 0.991 4.67 0.659 25 :1@C2_:2@C4 200622 0.991 4.48 0.848 26 :1@C5_:2@O6 200543 0.991 4.22 0.681 27 :1@N1_:2@N1 200490 0.99 4.29 0.643 28 :1@C4_:2@N3 200479 0.99 4.91 0.559 29 :1@N3_:2@C6 200437 0.99 4.76 0.857 30 :1@C2_:2@C5 200351 0.99 4.51 0.621 31 :1@C6_:2@N1 200334 0.99 4.2 0.598 32 :1@C4_:2@O6 200330 0.99 4.84 0.899 33 :1@C5_:2@N7 200329 0.99 4.38 0.852 34 :1@O6_:2@C6 200279 0.989 4.18 0.761 35 :1@O6_:2@O6 199999 0.988 4 0.635 36 :1@C8_:2@C5 199993 0.988 4.79 0.648 37 :1@C5_:2@N1 199986 0.988 4.5 0.711 38 :1@C2_:2@N1 199854 0.987 4.65 0.839 39 :1@N7_:2@C6 199835 0.987 4.49 0.699 40 :1@C2_:2@C2 199772 0.987 4.67 0.726 41 :1@N7_:2@C5 199747 0.987 4.56 0.709 42 :1@C2_:2@C6 199703 0.987 4.6 0.745 43 :1@N3_:2@C8 199682 0.986 4.68 0.937 44 :1@N1_:2@C2 199617 0.986 4.53 0.861 45 :1@N7_:2@O6 199590 0.986 4.45 0.729 46 :1@O6_:2@N1 199535 0.986 4.32 0.887 47 :1@C2_:2@N3 199522 0.986 4.6 0.846 48 :1@N3_:2@C2 199468 0.985 4.95 0.782 49 :1@N9_:2@C6 199357 0.985 5.05 0.819 50 :1@C4_:2@N1 199288 0.985 4.83 0.902 51 :1@N1_:2@O6 199083 0.983 4.47 0.89 52 :1@C6_:2@C2 199034 0.983 4.69 0.838 53 :1@N3_:2@N1 198917 0.983 4.95 1 54 :1@C8_:2@C4 198865 0.982 5.28 0.639 55 :1@C5_:2@N3 198773 0.982 5.08 0.722 56 :1@C4_:2@C2 198679 0.981 5.03 0.768 57 :1@N1_:2@C4 198635 0.981 4.64 1.11 58 :1@C6_:2@C4 198503 0.981 4.77 1.06 59 :1@N7_:2@C4 198335 0.98 5.2 0.732 60 :1@C8_:2@C6 198300 0.98 5 0.769 61 :1@C5_:2@C2 198250 0.979 4.95 0.716 62 :1@C6_:2@N7 197369 0.975 4.76 0.958 63 :1@C8_:2@O6 197023 0.973 5.12 0.791 64 :1@O6_:2@C5 196600 0.971 4.76 1 65 :1@C2_:2@N7 196516 0.971 4.91 0.837 66 :1@N1_:2@N3 196209 0.969 4.69 1.14 67 :1@C8_:2@N9 196168 0.969 5.44 0.641 68 :1@C5_:2@N9 195967 0.968 5.09 0.973 69 :1@N2_:2@C5 195466 0.966 5.11 0.717 70 :1@C8_:2@N7 195267 0.965 4.55 0.81 71 :1@C2_:2@O6 194911 0.963 4.99 1.09 72 :1@C6_:2@N3 194846 0.963 4.97 1.04 73 :1@C5_:2@C8 194755 0.962 4.86 1.01 74 :1@N2_:2@C4 194751 0.962 4.86 0.886 75 :1@N1_:2@N7 194512 0.961 4.96 0.933 76 :1@N7_:2@N1 194498 0.961 4.98 0.919 77 :1@N9_:2@O6 194462 0.961 5.37 0.85 78 :1@N9_:2@N3 194229 0.96 5.41 0.795 79 :1@N7_:2@N7 193868 0.958 4.5 0.864 80 :1@N3_:2@O6 193268 0.955 5.22 1.08 81 :1@N2_:2@C6 193138 0.954 5.22 0.871 82 :1@N2_:2@N1 192389 0.95 5.08 0.983 83 :1@C2_:2@N2 191747 0.947 5.14 0.868 84 :1@N2_:2@C2 191416 0.946 4.88 0.889 85 :1@C2_:2@N9 191314 0.945 4.75 1.18 86 :1@N1_:2@N2 191045 0.944 4.95 0.909 87 :1@N2_:2@N3 190798 0.943 4.74 0.932 88 :1@C8_:2@C8 189923 0.938 4.9 0.786 89 :1@O6_:2@C2 189507 0.936 4.88 1.12 90 :1@C6_:2@N2 189490 0.936 5.23 0.846 91 :1@C2_:2@C8 186806 0.923 4.95 1.05 92 :1@N7_:2@N9 185815 0.918 5.52 0.774 93 :1@N3_:2@N2 185332 0.916 5.51 0.897 94 :1@N7_:2@C8 183690 0.907 5.03 0.84 95 :1@N7_:2@N3 183354 0.906 5.63 0.769 96 :1@O6_:2@N7 183293 0.905 5.2 0.968 97 :1@N7_:2@C2 182247 0.9 5.44 0.934 98 :1@C5_:2@N2 180844 0.893 5.55 0.796 99 :1@N2_:2@N7 178272 0.881 5.41 0.892 100 :1@N9_:2@N1 177719 0.878 5.32 1.01 101 :1@C8_:2@N1 177068 0.875 5.36 0.992 102 :1@C8_:2@N3 176470 0.872 5.72 0.836 103 :1@C6_:2@C8 175498 0.867 5.16 1.04 104 :1@C4_:2@N2 173500 0.857 5.59 0.832 105 :1@O6_:2@C4 172537 0.852 5.11 1.1 106 :1@N2_:2@N9 172213 0.851 4.89 1.09 107 :1@N2_:2@N2 171615 0.848 4.97 0.985 108 :1@N9_:2@C2 170825 0.844 5.43 0.995 109 :1@N1_:2@C8 169096 0.835 5.11 1.04 110 :1@O6_:2@N2 168970 0.835 5.17 1.06 111 :1@N1_:2@N9 168359 0.832 4.91 1.17 112 :1@C6_:2@N9 166009 0.82 5.11 1.07 113 :1@O6_:2@N3 161371 0.797 5.12 1.11 114 :1@N2_:2@C8 159305 0.787 5.17 0.908 115 :1@C8_:2@C2 157294 0.777 5.55 1.05 116 :1@N2_:2@O6 156379 0.773 5.36 1.11 117 :1@O6_:2@C8 133650 0.66 5.43 0.775 118 :1@O6_:2@N9 123929 0.612 5.32 0.73 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0141 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 202425 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 202425 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 202425 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 202425 COM "COM" (double, distance), size is 202425 v_base1 "v_base1" (vector), size is 202425 v_base2 "v_base2" (vector), size is 202425 normalangle "normalangle" (double), size is 202425 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 1.7629 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.