CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:16:05 | Available memory: 52189 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,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, 101795 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 101795 of 101795) Coordinate processing will occur on 101795 frames. TIME: Run Initialization took 0.0001 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.c2 (1-101795, 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 86 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@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@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@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@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@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@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@N3' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 101795 frames and processed 101795 frames. TIME: Trajectory processing: 0.6064 s TIME: Avg. throughput= 167877.7104 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 82.8132 86 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N9 101391 0.996 4.31 0.557 2 :1@N9_:2@N9 101342 0.996 4.75 0.456 3 :1@N9_:2@C8 101320 0.995 4.28 0.535 4 :1@C4_:2@C8 101274 0.995 4.09 0.687 5 :1@C5_:2@N9 101174 0.994 4.46 0.599 6 :1@C4_:2@C4 101159 0.994 4.49 0.503 7 :1@C4_:2@N7 101105 0.993 4.18 0.666 8 :1@C4_:2@C5 101024 0.992 4.41 0.531 9 :1@C5_:2@C4 100984 0.992 4.3 0.531 10 :1@N9_:2@N7 100959 0.992 4.41 0.571 11 :1@C6_:2@C4 100866 0.991 4.14 0.63 12 :1@C5_:2@C5 100778 0.99 4.01 0.52 13 :1@C5_:2@C8 100757 0.99 4.25 0.663 14 :1@N9_:2@C4 100705 0.989 5.13 0.54 15 :1@C5_:2@N7 100696 0.989 4 0.684 16 :1@C8_:2@C8 100606 0.988 4.49 0.653 17 :1@N9_:2@C5 100602 0.988 4.93 0.546 18 :1@C6_:2@C5 100498 0.987 3.96 0.658 19 :1@C8_:2@N9 100388 0.986 5.06 0.734 20 :1@C6_:2@N9 100360 0.986 4.58 0.729 21 :1@C6_:2@N3 100315 0.985 4.42 0.665 22 :1@C5_:2@N3 100309 0.985 4.88 0.667 23 :1@N7_:2@C8 100304 0.985 4.53 0.668 24 :1@N7_:2@N7 100296 0.985 4.13 0.722 25 :1@N3_:2@C4 100278 0.985 4.55 0.744 26 :1@N7_:2@C5 100201 0.984 4.33 0.724 27 :1@N7_:2@N9 100192 0.984 4.94 0.775 28 :1@N7_:2@C4 100174 0.984 4.82 0.828 29 :1@C8_:2@N7 100122 0.984 4.32 0.71 30 :1@C4_:2@N3 100095 0.983 5.16 0.599 31 :1@C5_:2@C6 100071 0.983 4.39 0.593 32 :1@N1_:2@C4 100061 0.983 4.15 0.86 33 :1@N6_:2@C4 100050 0.983 4.51 0.697 34 :1@N6_:2@C5 99965 0.982 4.21 0.692 35 :1@C6_:2@C6 99942 0.982 4.05 0.641 36 :1@C6_:2@N7 99918 0.982 4.32 0.824 37 :1@N3_:2@N9 99904 0.981 4.27 0.824 38 :1@N3_:2@C8 99877 0.981 4.31 0.881 39 :1@C6_:2@C2 99876 0.981 4.44 0.642 40 :1@N3_:2@C5 99859 0.981 4.73 0.712 41 :1@C4_:2@C6 99772 0.98 5.07 0.595 42 :1@C8_:2@C4 99748 0.98 5.23 0.805 43 :1@C8_:2@C5 99735 0.98 4.81 0.745 44 :1@N1_:2@C5 99723 0.98 4.25 0.888 45 :1@N6_:2@C6 99685 0.979 3.91 0.689 46 :1@C6_:2@N1 99663 0.979 4.32 0.618 47 :1@C5_:2@C2 99620 0.979 5.09 0.721 48 :1@N6_:2@C2 99597 0.978 4.28 0.761 49 :1@N6_:2@N1 99592 0.978 3.99 0.66 50 :1@N3_:2@N7 99591 0.978 4.6 0.823 51 :1@C5_:2@N1 99414 0.977 4.93 0.685 52 :1@C6_:2@C8 99410 0.977 4.63 0.781 53 :1@N7_:2@C6 98923 0.972 4.65 0.824 54 :1@C5_:2@N6 98913 0.972 4.74 0.694 55 :1@C2_:2@C4 98848 0.971 4.28 0.892 56 :1@N6_:2@N6 98743 0.97 4.12 0.889 57 :1@C6_:2@N6 98645 0.969 4.45 0.785 58 :1@C2_:2@C5 98618 0.969 4.54 0.882 59 :1@N1_:2@N1 98488 0.968 4.51 0.807 60 :1@N1_:2@C6 98481 0.967 4.4 0.853 61 :1@N6_:2@N7 98402 0.967 4.78 0.802 62 :1@N1_:2@N9 97671 0.959 4.49 0.879 63 :1@C4_:2@N1 97370 0.957 5.63 0.672 64 :1@N1_:2@N7 97341 0.956 4.66 0.945 65 :1@N9_:2@C6 97110 0.954 5.67 0.658 66 :1@N6_:2@N9 96702 0.95 5.17 0.679 67 :1@C2_:2@N9 96561 0.949 4.25 0.895 68 :1@N7_:2@N1 96557 0.949 5.32 0.949 69 :1@C4_:2@N6 96380 0.947 5.53 0.613 70 :1@C2_:2@C8 96226 0.945 4.54 0.934 71 :1@C2_:2@N7 96222 0.945 4.7 0.937 72 :1@N3_:2@C6 96088 0.944 5.39 0.652 73 :1@N6_:2@C8 96021 0.943 5.27 0.697 74 :1@N1_:2@C8 95908 0.942 4.74 0.886 75 :1@C8_:2@C6 95865 0.942 5.35 0.83 76 :1@N7_:2@N6 95642 0.94 4.71 0.782 77 :1@C2_:2@C6 95631 0.939 4.98 0.805 78 :1@N7_:2@N3 95171 0.935 5.45 0.99 79 :1@N1_:2@N6 93592 0.919 4.89 0.869 80 :1@C8_:2@N6 91732 0.901 5.48 0.787 81 :1@N7_:2@C2 90411 0.888 5.54 0.986 82 :1@N9_:2@N6 88094 0.865 5.97 0.619 83 :1@C2_:2@N6 86089 0.846 5.49 0.778 84 :1@N3_:2@N6 85153 0.837 5.89 0.602 85 :1@C8_:2@N3 79577 0.782 5.8 0.878 86 :1@C8_:2@N1 73452 0.722 5.83 0.872 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0053 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 101795 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 101795 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 101795 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 101795 COM "COM" (double, distance), size is 101795 v_base1 "v_base1" (vector), size is 101795 v_base2 "v_base2" (vector), size is 101795 normalangle "normalangle" (double), size is 101795 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: 0.7936 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.