CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/10/16 11:34:18 | Available memory: 6519.85 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/full.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/full.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] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 88440 frames INPUT TRAJECTORIES: 0: 'ctraj.c0' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 88440 of 88440) Coordinate processing will occur on 88440 frames. TIME: Run Initialization took 0.0011 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 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] 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 (1-88440, 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 52 native contacts: Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C5' to ':2@C6' 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@C6' 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@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' 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@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' 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 88440 frames and processed 88440 frames. TIME: Trajectory processing: 6.6892 s TIME: Avg. throughput= 13221.3594 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 50.8772 52 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 88374 0.999 4.38 0.537 2 :1@C4_:2@C5 88280 0.998 4.28 0.6 3 :1@N3_:2@C4 88098 0.996 4.33 0.523 4 :1@C4_:2@C6 88010 0.995 4.48 0.595 5 :1@N3_:2@N9 87933 0.994 4.44 0.562 6 :1@C4_:2@N9 87920 0.994 4.71 0.576 7 :1@N9_:2@C4 87907 0.994 4.9 0.647 8 :1@N3_:2@C5 87881 0.994 4.54 0.619 9 :1@N3_:2@N3 87846 0.993 4.57 0.63 10 :1@C4_:2@N3 87766 0.992 4.66 0.676 11 :1@C2_:2@C4 87695 0.992 4.33 0.649 12 :1@C5_:2@C6 87652 0.991 4.14 0.685 13 :1@N9_:2@C5 87605 0.991 4.51 0.681 14 :1@C4_:2@N1 87575 0.99 4.74 0.665 15 :1@C2_:2@N3 87555 0.99 4.26 0.643 16 :1@C5_:2@C4 87486 0.989 4.48 0.645 17 :1@C5_:2@N1 87461 0.989 4.19 0.703 18 :1@N3_:2@C6 87439 0.989 4.97 0.665 19 :1@N3_:2@C2 87410 0.988 4.95 0.735 20 :1@C4_:2@C2 87309 0.987 4.77 0.749 21 :1@C6_:2@C2 87292 0.987 4.02 0.669 22 :1@N1_:2@N3 87283 0.987 4.13 0.604 23 :1@C6_:2@N1 87273 0.987 4.1 0.667 24 :1@N1_:2@C2 87244 0.986 4.17 0.671 25 :1@C2_:2@C2 87230 0.986 4.59 0.738 26 :1@N1_:2@C4 87159 0.986 4.45 0.646 27 :1@N3_:2@N1 87157 0.985 5.18 0.723 28 :1@C5_:2@C2 87121 0.985 4.34 0.788 29 :1@C2_:2@N9 86993 0.984 4.58 0.636 30 :1@C2_:2@C5 86921 0.983 4.74 0.766 31 :1@N9_:2@C6 86895 0.983 4.71 0.682 32 :1@N3_:2@C8 86848 0.982 4.69 0.728 33 :1@C6_:2@C4 86749 0.981 4.49 0.598 34 :1@C5_:2@N3 86698 0.98 4.53 0.73 35 :1@C6_:2@N3 86688 0.98 4.24 0.623 36 :1@C6_:2@C6 86678 0.98 4.34 0.734 37 :1@C4_:2@N7 86610 0.979 4.53 0.771 38 :1@N3_:2@N7 86547 0.979 4.77 0.75 39 :1@N1_:2@N1 86476 0.978 4.53 0.759 40 :1@C2_:2@N1 86189 0.975 4.99 0.803 41 :1@N6_:2@C2 86059 0.973 4.1 0.737 42 :1@N1_:2@C5 85894 0.971 4.79 0.792 43 :1@C2_:2@C6 85748 0.97 5.03 0.807 44 :1@N1_:2@C6 85427 0.966 4.78 0.823 45 :1@N1_:2@N9 85391 0.966 4.97 0.59 46 :1@C2_:2@C8 85362 0.965 5.1 0.767 47 :1@N6_:2@N3 85230 0.964 4.59 0.684 48 :1@C2_:2@N7 84156 0.952 5.2 0.819 49 :1@N9_:2@N3 83920 0.949 5.32 0.751 50 :1@N3_:2@N6 83373 0.943 5.59 0.714 51 :1@N9_:2@C2 80552 0.911 5.32 0.794 52 :1@C2_:2@N6 75211 0.85 5.63 0.811 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0073 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 88440 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 88440 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 88440 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 88440 COM "COM" (double, distance), size is 88440 v_base1 "v_base1" (vector), size is 88440 v_base2 "v_base2" (vector), size is 88440 normalangle "normalangle" (double), size is 88440 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: 6.9036 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.