CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 19:19:25 | Available memory: 49738.7 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,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_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,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. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 81258 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 81258 of 81258) Coordinate processing will occur on 81258 frames. TIME: Run Initialization took 0.0006 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*](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] Vector 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] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c0 (1-81258, 1) ----- 0% 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' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 81258 frames and processed 81258 frames. TIME: Trajectory processing: 0.5006 s TIME: Avg. throughput= 162308.8939 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 98.1798 100 # Contact Nframes Frac. Avg Stdev 1 :1@C6_:2@N1 81258 1 4.03 0.503 2 :1@C6_:2@C6 81258 1 4.09 0.586 3 :1@C4_:2@C5 81258 1 4.13 0.386 4 :1@C4_:2@N7 81258 1 4.17 0.631 5 :1@C6_:2@C5 81258 1 4.23 0.599 6 :1@C6_:2@C4 81258 1 4.27 0.382 7 :1@N3_:2@N9 81258 1 4.28 0.378 8 :1@N3_:2@C4 81258 1 4.35 0.418 9 :1@C4_:2@C4 81258 1 4.39 0.417 10 :1@C4_:2@C8 81258 1 4.43 0.595 11 :1@C4_:2@N9 81258 1 4.59 0.36 12 :1@N1_:2@N9 81258 1 4.68 0.476 13 :1@N6_:2@N1 81257 1 3.91 0.537 14 :1@C5_:2@C5 81257 1 4.03 0.461 15 :1@N1_:2@N3 81257 1 4.05 0.457 16 :1@N1_:2@C4 81257 1 4.19 0.468 17 :1@C6_:2@N9 81257 1 4.97 0.459 18 :1@N3_:2@C8 81256 1 4.35 0.645 19 :1@C5_:2@C4 81256 1 4.39 0.488 20 :1@N3_:2@C5 81256 1 4.44 0.493 21 :1@C2_:2@N9 81254 1 4.32 0.494 22 :1@C5_:2@C6 81253 1 3.98 0.46 23 :1@C6_:2@N3 81252 1 4.22 0.56 24 :1@C4_:2@C6 81251 1 4.49 0.48 25 :1@C2_:2@C4 81248 1 4.19 0.527 26 :1@C6_:2@C2 81245 1 4.05 0.61 27 :1@N6_:2@C4 81244 1 4.81 0.499 28 :1@C5_:2@N6 81243 1 4.26 0.565 29 :1@N3_:2@N3 81232 1 4.84 0.578 30 :1@N3_:2@N7 81231 1 4.47 0.681 31 :1@N1_:2@C2 81229 1 4.19 0.595 32 :1@N6_:2@C2 81227 1 3.98 0.624 33 :1@C2_:2@N3 81227 1 4.35 0.571 34 :1@C4_:2@N6 81216 0.999 4.88 0.521 35 :1@N9_:2@N7 81211 0.999 4.26 0.566 36 :1@N9_:2@C5 81209 0.999 4.5 0.544 37 :1@C5_:2@N1 81204 0.999 4.29 0.678 38 :1@C5_:2@N9 81196 0.999 4.95 0.476 39 :1@C5_:2@N7 81191 0.999 4.42 0.755 40 :1@C2_:2@C5 81188 0.999 4.55 0.703 41 :1@N3_:2@C6 81184 0.999 5.05 0.537 42 :1@C2_:2@C8 81182 0.999 4.74 0.76 43 :1@N6_:2@N3 81179 0.999 4.48 0.626 44 :1@N1_:2@C5 81176 0.999 4.5 0.756 45 :1@N1_:2@N1 81161 0.999 4.51 0.689 46 :1@N9_:2@C8 81151 0.999 4.68 0.552 47 :1@C4_:2@N3 81141 0.999 4.94 0.678 48 :1@N6_:2@C6 81116 0.998 4.26 0.725 49 :1@C5_:2@C8 81097 0.998 4.92 0.669 50 :1@C2_:2@C2 81078 0.998 4.8 0.672 51 :1@N7_:2@N6 81076 0.998 3.96 0.67 52 :1@C4_:2@N1 81068 0.998 5 0.678 53 :1@N7_:2@C6 81038 0.997 4.08 0.722 54 :1@N6_:2@C5 81033 0.997 4.75 0.702 55 :1@N9_:2@N9 81020 0.997 5.17 0.458 56 :1@C5_:2@N3 81003 0.997 4.69 0.757 57 :1@N7_:2@C5 81001 0.997 4.38 0.642 58 :1@C5_:2@C2 80938 0.996 4.56 0.844 59 :1@N1_:2@C6 80918 0.996 4.63 0.79 60 :1@N9_:2@C4 80906 0.996 5.06 0.6 61 :1@N9_:2@C6 80875 0.995 4.84 0.694 62 :1@C2_:2@C6 80784 0.994 5.03 0.713 63 :1@C2_:2@N1 80753 0.994 5.15 0.685 64 :1@N3_:2@C2 80745 0.994 5.31 0.654 65 :1@N3_:2@N1 80737 0.994 5.46 0.606 66 :1@N7_:2@N7 80726 0.993 4.66 0.747 67 :1@C2_:2@N7 80717 0.993 4.9 0.841 68 :1@C6_:2@C8 80716 0.993 5.28 0.715 69 :1@N1_:2@C8 80691 0.993 5.2 0.763 70 :1@C8_:2@N7 80677 0.993 4.52 0.677 71 :1@N9_:2@N6 80650 0.993 4.95 0.659 72 :1@C6_:2@N6 80624 0.992 4.58 0.802 73 :1@C6_:2@N7 80562 0.991 4.91 0.858 74 :1@C4_:2@C2 80544 0.991 5.13 0.767 75 :1@C8_:2@C5 80528 0.991 4.58 0.683 76 :1@C8_:2@N6 80382 0.989 4.36 0.783 77 :1@N6_:2@N9 80233 0.987 5.71 0.528 78 :1@C8_:2@C6 80107 0.986 4.53 0.831 79 :1@N7_:2@N1 79919 0.984 4.48 0.972 80 :1@N7_:2@C4 79815 0.982 5.03 0.695 81 :1@C8_:2@C8 79712 0.981 5.23 0.615 82 :1@N1_:2@N7 79640 0.98 5.12 0.894 83 :1@N3_:2@N6 79552 0.979 5.67 0.557 84 :1@N6_:2@N6 79520 0.979 4.6 0.966 85 :1@N7_:2@C8 79386 0.977 5.41 0.66 86 :1@C8_:2@C4 78299 0.964 5.3 0.699 87 :1@N7_:2@N9 78213 0.963 5.64 0.565 88 :1@C8_:2@N9 77752 0.957 5.69 0.539 89 :1@N1_:2@N6 76191 0.938 5.27 0.847 90 :1@N7_:2@C2 75653 0.931 4.98 1.01 91 :1@N6_:2@N7 75463 0.929 5.54 0.835 92 :1@N7_:2@N3 74880 0.922 5.32 0.874 93 :1@N9_:2@N1 74460 0.916 5.44 0.786 94 :1@C8_:2@N1 73984 0.91 5.07 0.945 95 :1@N9_:2@N3 73786 0.908 5.68 0.717 96 :1@C2_:2@N6 73540 0.905 5.69 0.676 97 :1@N6_:2@C8 69334 0.853 5.95 0.622 98 :1@N9_:2@C2 66944 0.824 5.67 0.752 99 :1@C8_:2@N3 65298 0.804 5.69 0.767 100 :1@C8_:2@C2 64339 0.792 5.46 0.868 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0070 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 81258 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 81258 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 81258 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 81258 COM "COM" (double, distance), size is 81258 v_base1 "v_base1" (vector), size is 81258 v_base2 "v_base2" (vector), size is 81258 normalangle "normalangle" (double), size is 81258 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: 0.7014 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.