CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 13:31:39 | Available memory: 54525.6 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.c2] Reading '../ctraj.c2' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,N4,N3,C2,O2' Mask2=':2@N1,C6,C5,C4,N4,N3,C2,O2', 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,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] [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', 61 atoms, 2 res, box: Orthogonal, 1 mol, 60535 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 60535 of 60535) Coordinate processing will occur on 60535 frames. TIME: Run Initialization took 0.0004 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*](37) Reference mask: [:1,2&!@H*](37) 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,C6,C5,C4,N4,N3,C2,O2 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Vector mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c2 (1-60535, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 64 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@N4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@N4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@N4' to ':2@N1' Atom ':1@N4' to ':2@C6' Atom ':1@N4' to ':2@C5' Atom ':1@N4' to ':2@C4' Atom ':1@N4' to ':2@N4' Atom ':1@N4' to ':2@N3' Atom ':1@N4' to ':2@C2' Atom ':1@N4' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@N4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@N4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@N4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 60535 frames and processed 60535 frames. TIME: Trajectory processing: 0.2923 s TIME: Avg. throughput= 207118.7113 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 44.4238 64 # Contact Nframes Frac. Avg Stdev 1 :1@C6_:2@C6 52429 0.866 5.22 0.913 2 :1@N1_:2@C6 51883 0.857 5.08 0.926 3 :1@C6_:2@N1 49143 0.812 5.43 0.818 4 :1@C5_:2@C6 48830 0.807 5.26 0.905 5 :1@C6_:2@C5 48282 0.798 4.98 0.982 6 :1@N1_:2@C5 47783 0.789 4.78 0.899 7 :1@C2_:2@C6 47500 0.785 4.87 1.04 8 :1@C2_:2@C5 47361 0.782 4.61 1.08 9 :1@C5_:2@N1 47047 0.777 5.31 0.895 10 :1@N1_:2@N1 46797 0.773 5.4 0.719 11 :1@C5_:2@C5 46031 0.76 4.97 0.998 12 :1@N3_:2@C5 45193 0.747 4.61 1.08 13 :1@C4_:2@C6 45073 0.745 5.12 0.873 14 :1@O2_:2@C5 44763 0.739 4.67 1.11 15 :1@C4_:2@C5 44449 0.734 4.8 0.988 16 :1@N3_:2@C6 44289 0.732 4.9 0.963 17 :1@N1_:2@C4 43843 0.724 5.03 0.726 18 :1@C5_:2@C2 43712 0.722 5.19 0.98 19 :1@C4_:2@N1 43658 0.721 5.13 0.832 20 :1@O2_:2@C6 43652 0.721 4.87 1.06 21 :1@C2_:2@C4 43476 0.718 4.67 0.899 22 :1@C6_:2@C4 43230 0.714 5.04 0.892 23 :1@C2_:2@N1 42765 0.706 5.09 0.868 24 :1@N3_:2@C4 42748 0.706 4.39 1.01 25 :1@C6_:2@C2 42519 0.702 5.46 0.833 26 :1@C5_:2@C4 42510 0.702 4.78 0.991 27 :1@C4_:2@C4 42370 0.7 4.47 0.986 28 :1@C2_:2@N4 42364 0.7 4.87 0.812 29 :1@N3_:2@N4 42268 0.698 4.52 0.953 30 :1@N1_:2@N4 42196 0.697 5.3 0.721 31 :1@C4_:2@C2 42108 0.696 4.86 0.943 32 :1@N3_:2@N1 41815 0.691 4.97 0.887 33 :1@C4_:2@N4 41476 0.685 4.55 0.999 34 :1@O2_:2@C4 41469 0.685 4.84 0.992 35 :1@C5_:2@N3 41445 0.685 4.92 0.968 36 :1@C4_:2@N3 41097 0.679 4.53 0.963 37 :1@C6_:2@N3 41076 0.679 5.31 0.844 38 :1@N1_:2@N3 41021 0.678 5.4 0.686 39 :1@N1_:2@C2 41002 0.677 5.53 0.688 40 :1@N4_:2@C2 40666 0.672 4.91 0.955 41 :1@N4_:2@N1 40661 0.672 5.39 0.806 42 :1@N3_:2@N3 40522 0.669 4.5 0.947 43 :1@C2_:2@N3 40434 0.668 4.95 0.824 44 :1@N3_:2@C2 40243 0.665 4.78 0.941 45 :1@N4_:2@C4 40084 0.662 4.59 0.971 46 :1@N4_:2@C5 40053 0.662 5.12 0.869 47 :1@O2_:2@N4 40036 0.661 5 0.997 48 :1@N4_:2@C6 39848 0.658 5.49 0.76 49 :1@C5_:2@N4 39836 0.658 4.83 1.07 50 :1@C6_:2@N4 39833 0.658 5.19 0.969 51 :1@N4_:2@N3 39766 0.657 4.5 0.989 52 :1@C2_:2@C2 39597 0.654 5.11 0.835 53 :1@N4_:2@N4 39413 0.651 4.55 1.04 54 :1@C4_:2@O2 39350 0.65 5.16 0.914 55 :1@O2_:2@N1 39187 0.647 5.16 0.992 56 :1@N4_:2@O2 38851 0.642 5.06 0.98 57 :1@C5_:2@O2 38266 0.632 5.42 0.943 58 :1@O2_:2@N3 37939 0.627 5.16 0.881 59 :1@N3_:2@O2 36911 0.61 5.15 0.901 60 :1@O2_:2@C2 36469 0.602 5.27 0.915 61 :1@C6_:2@O2 34629 0.572 5.77 0.857 62 :1@C2_:2@O2 34354 0.568 5.55 0.831 63 :1@N1_:2@O2 32995 0.545 5.96 0.787 64 :1@O2_:2@O2 28579 0.472 5.57 0.852 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0031 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 60535 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 60535 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 60535 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 60535 COM "COM" (double, distance), size is 60535 v_base1 "v_base1" (vector), size is 60535 v_base2 "v_base2" (vector), size is 60535 normalangle "normalangle" (double), size is 60535 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: 0.4205 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.