CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 18:09:48 | Available memory: 52498.5 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,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, 127823 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 127823 of 127823) Coordinate processing will occur on 127823 frames. TIME: Run Initialization took 0.0005 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.c1 (1-127823, 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 127823 frames and processed 127823 frames. TIME: Trajectory processing: 0.6027 s TIME: Avg. throughput= 212079.7329 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 52.4573 64 # Contact Nframes Frac. Avg Stdev 1 :1@C2_:2@C5 126514 0.99 4.25 0.648 2 :1@N1_:2@C5 126501 0.99 4.42 0.562 3 :1@N1_:2@C6 126474 0.989 4.81 0.549 4 :1@O2_:2@C5 126287 0.988 4.31 0.793 5 :1@C2_:2@C6 125949 0.985 4.8 0.673 6 :1@O2_:2@C6 125680 0.983 4.72 0.78 7 :1@O2_:2@C4 125298 0.98 4.38 0.725 8 :1@C2_:2@C4 125293 0.98 4.37 0.685 9 :1@C2_:2@N4 124821 0.977 4.4 0.75 10 :1@N3_:2@C5 124804 0.976 4.53 0.794 11 :1@O2_:2@N4 124636 0.975 4.54 0.81 12 :1@N1_:2@C4 124497 0.974 4.78 0.748 13 :1@C6_:2@C5 124191 0.972 4.81 0.796 14 :1@N1_:2@N1 123431 0.966 5.46 0.584 15 :1@O2_:2@N1 123315 0.965 5.11 0.784 16 :1@N3_:2@N4 123279 0.964 4.11 0.869 17 :1@N3_:2@C4 123275 0.964 4.42 0.852 18 :1@C2_:2@N1 122948 0.962 5.37 0.686 19 :1@C6_:2@C6 122830 0.961 5.33 0.704 20 :1@N1_:2@N4 122431 0.958 4.94 0.819 21 :1@O2_:2@N3 122406 0.958 4.74 0.852 22 :1@C4_:2@C5 121625 0.952 4.88 0.858 23 :1@C2_:2@N3 120992 0.947 4.9 0.836 24 :1@N3_:2@C6 120637 0.944 5.31 0.744 25 :1@O2_:2@C2 120280 0.941 5.07 0.867 26 :1@C5_:2@C5 119160 0.932 4.99 0.867 27 :1@C4_:2@N4 118819 0.93 4.3 1.01 28 :1@C2_:2@C2 117238 0.917 5.34 0.777 29 :1@C4_:2@C4 117213 0.917 4.74 0.92 30 :1@N3_:2@N3 115037 0.9 4.96 0.913 31 :1@C6_:2@C4 114355 0.895 5.03 0.869 32 :1@N1_:2@N3 114288 0.894 5.26 0.829 33 :1@N4_:2@N4 114048 0.892 4.44 1.07 34 :1@C6_:2@N4 111766 0.874 4.98 0.933 35 :1@C4_:2@C6 111053 0.869 5.67 0.711 36 :1@C5_:2@N4 110350 0.863 4.67 0.991 37 :1@N1_:2@C2 110260 0.863 5.55 0.692 38 :1@N4_:2@C5 109809 0.859 5.38 0.814 39 :1@C5_:2@C6 109166 0.854 5.66 0.699 40 :1@C5_:2@C4 108685 0.85 4.96 0.863 41 :1@N4_:2@C4 106113 0.83 5.05 0.883 42 :1@N3_:2@N1 105772 0.827 5.78 0.708 43 :1@C6_:2@N1 101754 0.796 5.87 0.578 44 :1@N3_:2@C2 101630 0.795 5.53 0.774 45 :1@O2_:2@O2 100156 0.784 5.45 0.905 46 :1@C4_:2@N3 100136 0.783 5.23 0.778 47 :1@C6_:2@N3 96478 0.755 5.46 0.862 48 :1@C5_:2@N3 92573 0.724 5.49 0.793 49 :1@C2_:2@O2 90993 0.712 5.78 0.735 50 :1@N4_:2@N3 89019 0.696 5.54 0.743 51 :1@C6_:2@C2 87734 0.686 5.84 0.701 52 :1@C4_:2@C2 85508 0.669 5.9 0.611 53 :1@C4_:2@N1 83046 0.65 6.09 0.552 54 :1@N1_:2@O2 80952 0.633 6 0.656 55 :1@C5_:2@N1 80951 0.633 6.15 0.515 56 :1@N4_:2@C6 77663 0.608 6.08 0.574 57 :1@C5_:2@C2 76394 0.598 6.02 0.607 58 :1@N3_:2@O2 74349 0.582 5.93 0.693 59 :1@N4_:2@C2 59724 0.467 6.18 0.521 60 :1@C4_:2@O2 51837 0.406 6.29 0.51 61 :1@C6_:2@O2 50714 0.397 6.1 0.72 62 :1@N4_:2@N1 45542 0.356 6.38 0.427 63 :1@C5_:2@O2 38093 0.298 6.27 0.64 64 :1@N4_:2@O2 28482 0.223 6.46 0.416 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0065 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 127823 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 127823 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 127823 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 127823 COM "COM" (double, distance), size is 127823 v_base1 "v_base1" (vector), size is 127823 v_base2 "v_base2" (vector), size is 127823 normalangle "normalangle" (double), size is 127823 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: 0.8384 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.