CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 11:40:07 | Available memory: 53096.4 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.c1] Reading '../ctraj.c1' 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, 13430 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 13430 of 13430) Coordinate processing will occur on 13430 frames. TIME: Run Initialization took 0.0000 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.c1 (1-13430, 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 67 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@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@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@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@C4' 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@N6' to ':2@N6' 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@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@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 13430 frames and processed 13430 frames. TIME: Trajectory processing: 0.0811 s TIME: Avg. throughput= 165577.6107 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 58.2962 67 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N1 13379 0.996 4.12 0.63 2 :1@N9_:2@C2 13356 0.994 4.54 0.636 3 :1@N9_:2@C6 13344 0.994 4.17 0.633 4 :1@N9_:2@N3 13323 0.992 5.04 0.638 5 :1@C8_:2@N1 13276 0.989 4.07 0.769 6 :1@N9_:2@C4 13272 0.988 5.05 0.57 7 :1@N9_:2@C5 13236 0.986 4.68 0.557 8 :1@C4_:2@C6 13233 0.985 4.69 0.742 9 :1@N9_:2@N6 13229 0.985 4.25 0.718 10 :1@C4_:2@N1 13202 0.983 4.88 0.785 11 :1@C8_:2@C2 13197 0.983 4.63 0.788 12 :1@C8_:2@C6 13134 0.978 4.29 0.714 13 :1@C4_:2@N6 13111 0.976 4.52 0.773 14 :1@C4_:2@C5 13045 0.971 5.15 0.636 15 :1@N3_:2@C6 13035 0.971 5.18 0.817 16 :1@C8_:2@N6 13015 0.969 4.17 0.889 17 :1@C4_:2@C2 12999 0.968 5.44 0.78 18 :1@N3_:2@C5 12937 0.963 5.39 0.709 19 :1@N7_:2@N1 12919 0.962 4.76 0.835 20 :1@C8_:2@N3 12857 0.957 5.34 0.764 21 :1@N3_:2@N1 12857 0.957 5.55 0.804 22 :1@N3_:2@N6 12828 0.955 5.03 0.875 23 :1@C8_:2@C5 12823 0.955 5.07 0.54 24 :1@C4_:2@C4 12810 0.954 5.7 0.616 25 :1@N9_:2@N7 12780 0.952 5.33 0.485 26 :1@C5_:2@N6 12777 0.951 4.61 0.82 27 :1@N7_:2@N6 12763 0.95 4.45 0.823 28 :1@N7_:2@C6 12750 0.949 4.85 0.675 29 :1@C5_:2@C6 12720 0.947 5.03 0.76 30 :1@C8_:2@C4 12677 0.944 5.49 0.581 31 :1@N9_:2@N9 12658 0.943 5.83 0.501 32 :1@C5_:2@N1 12646 0.942 5.15 0.91 33 :1@N3_:2@C4 12527 0.933 5.93 0.598 34 :1@C4_:2@N3 12520 0.932 5.87 0.696 35 :1@C4_:2@N7 12477 0.929 5.55 0.537 36 :1@N3_:2@N7 12409 0.924 5.54 0.648 37 :1@N9_:2@C8 12380 0.922 5.93 0.44 38 :1@N7_:2@C5 12172 0.906 5.7 0.504 39 :1@C8_:2@N7 12145 0.904 5.85 0.489 40 :1@N7_:2@C2 12126 0.903 5.4 0.897 41 :1@C5_:2@C5 12071 0.899 5.69 0.574 42 :1@N3_:2@C2 12028 0.896 6.01 0.705 43 :1@C6_:2@N6 11724 0.873 5.17 0.869 44 :1@C2_:2@N6 11318 0.843 5.36 1.01 45 :1@C4_:2@C8 11298 0.841 6.18 0.434 46 :1@N3_:2@C8 11270 0.839 6.07 0.497 47 :1@N3_:2@N3 11256 0.838 6.23 0.594 48 :1@C5_:2@N7 11036 0.822 6.11 0.447 49 :1@C5_:2@C2 11035 0.822 5.73 0.908 50 :1@C4_:2@N9 10932 0.814 6.29 0.468 51 :1@C2_:2@C6 10873 0.81 5.7 0.89 52 :1@C6_:2@C6 10851 0.808 5.69 0.788 53 :1@N3_:2@N9 10643 0.792 6.3 0.451 54 :1@N1_:2@N6 10582 0.788 5.44 0.973 55 :1@C2_:2@C5 10455 0.778 5.97 0.687 56 :1@N7_:2@N7 10416 0.776 6.29 0.414 57 :1@N6_:2@N6 10291 0.766 5.64 0.764 58 :1@C2_:2@N7 10181 0.758 6 0.584 59 :1@C5_:2@C4 9856 0.734 6.21 0.585 60 :1@N1_:2@C6 8943 0.666 5.85 0.85 61 :1@C6_:2@C5 8739 0.651 6.22 0.541 62 :1@C2_:2@N1 8365 0.623 5.91 0.922 63 :1@C6_:2@N7 7252 0.54 6.45 0.38 64 :1@N1_:2@C5 7057 0.525 6.22 0.585 65 :1@N1_:2@N7 7001 0.521 6.38 0.44 66 :1@C2_:2@C8 6569 0.489 6.47 0.386 67 :1@C2_:2@C4 5932 0.442 6.35 0.55 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0007 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 13430 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 13430 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 13430 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 13430 COM "COM" (double, distance), size is 13430 v_base1 "v_base1" (vector), size is 13430 v_base2 "v_base2" (vector), size is 13430 normalangle "normalangle" (double), size is 13430 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: 0.1339 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.