CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/23/15 17:34:16 | Available memory: 49839 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':1@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 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [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] [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] [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', 63 atoms, 2 res, box: Orthogonal, 1 mol, 83496 frames INPUT TRAJECTORIES: 0: 'ctraj.c2' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 83496 of 83496) Coordinate processing will occur on 83496 frames. TIME: Run Initialization took 0.0006 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*](39) Reference mask: [:1,2&!@H*](39) 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 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':1@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [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. 6: [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. ----- ctraj.c2 (1-83496, 1) ----- 0% Using first frame to determine native contacts. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 59 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C6' Atom ':2@C8' to ':1@C2' Atom ':2@C8' to ':1@O2' Atom ':2@N7' to ':1@N1' Atom ':2@N7' to ':1@C6' Atom ':2@N7' to ':1@N3' Atom ':2@N7' to ':1@C2' Atom ':2@N7' to ':1@O2' Atom ':2@C5' to ':1@N1' Atom ':2@C5' to ':1@C6' Atom ':2@C5' to ':1@C5' Atom ':2@C5' to ':1@C4' Atom ':2@C5' to ':1@N3' Atom ':2@C5' to ':1@C2' Atom ':2@C5' to ':1@O2' Atom ':2@C6' to ':1@N1' Atom ':2@C6' to ':1@C6' Atom ':2@C6' to ':1@C5' Atom ':2@C6' to ':1@C4' Atom ':2@C6' to ':1@N4' Atom ':2@C6' to ':1@N3' Atom ':2@C6' to ':1@C2' Atom ':2@C6' to ':1@O2' Atom ':2@N6' to ':1@N1' Atom ':2@N6' to ':1@C6' Atom ':2@N6' to ':1@C5' Atom ':2@N6' to ':1@C4' Atom ':2@N6' to ':1@N4' Atom ':2@N6' to ':1@N3' Atom ':2@N6' to ':1@C2' Atom ':2@N6' to ':1@O2' Atom ':2@N1' to ':1@N1' Atom ':2@N1' to ':1@C6' Atom ':2@N1' to ':1@C5' Atom ':2@N1' to ':1@C4' Atom ':2@N1' to ':1@N4' Atom ':2@N1' to ':1@N3' Atom ':2@N1' to ':1@C2' Atom ':2@N1' to ':1@O2' Atom ':2@C2' to ':1@N1' Atom ':2@C2' to ':1@C6' Atom ':2@C2' to ':1@C5' Atom ':2@C2' to ':1@C4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C2' Atom ':2@N3' to ':1@O2' Atom ':2@C4' to ':1@N1' Atom ':2@C4' to ':1@C6' Atom ':2@C4' to ':1@C5' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 83496 frames and processed 83496 frames. TIME: Trajectory processing: 0.4362 s TIME: Avg. throughput= 191412.3931 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 2 1 51.5571 59 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 81497 0.976 4.61 0.667 2 :2@N7_:1@N1 81087 0.971 4.99 0.734 3 :2@C6_:1@N1 81012 0.97 4.22 0.701 4 :2@N6_:1@N1 80748 0.967 4.13 0.745 5 :2@C4_:1@N1 80050 0.959 5.17 0.583 6 :2@N1_:1@N1 79459 0.952 4.46 0.717 7 :2@C6_:1@C6 79318 0.95 4.52 0.772 8 :2@N6_:1@C6 79283 0.95 4.32 0.857 9 :2@N6_:1@C2 79236 0.949 4.24 0.869 10 :2@C6_:1@C2 79110 0.947 4.54 0.712 11 :2@C6_:1@O2 79096 0.947 4.73 0.792 12 :2@C5_:1@C6 78913 0.945 5.02 0.701 13 :2@N6_:1@O2 78819 0.944 4.49 1.04 14 :2@C5_:1@C2 78776 0.943 5.07 0.671 15 :2@C5_:1@O2 78766 0.943 5.12 0.762 16 :2@C8_:1@N1 78181 0.936 5.64 0.637 17 :2@C2_:1@N1 78139 0.936 5 0.72 18 :2@N1_:1@C2 77893 0.933 4.77 0.812 19 :2@N1_:1@C6 77866 0.933 4.69 0.765 20 :2@N3_:1@N1 77761 0.931 5.41 0.625 21 :2@N9_:1@N1 77528 0.929 5.82 0.524 22 :2@N1_:1@O2 77033 0.923 4.96 0.937 23 :2@N7_:1@C6 76694 0.919 5.42 0.74 24 :2@N6_:1@N3 76394 0.915 4.57 0.843 25 :2@N7_:1@C2 76223 0.913 5.38 0.853 26 :2@N6_:1@C5 76213 0.913 4.61 0.888 27 :2@C4_:1@C6 76192 0.913 5.6 0.582 28 :2@C2_:1@C6 75970 0.91 5.29 0.722 29 :2@C4_:1@C2 75743 0.907 5.71 0.55 30 :2@C4_:1@O2 75723 0.907 5.71 0.564 31 :2@C6_:1@N3 75475 0.904 5.11 0.679 32 :2@N6_:1@C4 75255 0.901 4.73 0.814 33 :2@C6_:1@C5 75196 0.901 5.06 0.744 34 :2@C2_:1@C2 75171 0.9 5.41 0.855 35 :2@N1_:1@C5 74314 0.89 5.2 0.757 36 :2@N1_:1@N3 74305 0.89 5.29 0.787 37 :2@N7_:1@O2 74234 0.889 5.26 1.1 38 :2@N3_:1@C6 73682 0.882 5.77 0.605 39 :2@C6_:1@C4 73525 0.881 5.33 0.679 40 :2@N1_:1@C4 72346 0.866 5.46 0.726 41 :2@C2_:1@O2 72343 0.866 5.44 1.02 42 :2@N3_:1@C2 71591 0.857 5.9 0.69 43 :2@C5_:1@C5 70773 0.848 5.73 0.641 44 :2@C5_:1@N3 70707 0.847 5.78 0.585 45 :2@N6_:1@N4 69356 0.831 5.38 0.764 46 :2@N3_:1@O2 69234 0.829 5.86 0.795 47 :2@C8_:1@C6 68195 0.817 6.06 0.607 48 :2@C2_:1@C5 66552 0.797 5.87 0.675 49 :2@N9_:1@C6 65782 0.788 6.22 0.493 50 :2@C5_:1@C4 64767 0.776 6.02 0.559 51 :2@C8_:1@C2 63429 0.76 6 0.676 52 :2@C2_:1@N3 62638 0.75 5.93 0.78 53 :2@C6_:1@N4 60440 0.724 6.02 0.585 54 :2@C8_:1@O2 59906 0.717 5.75 0.846 55 :2@N7_:1@N3 59028 0.707 5.98 0.682 56 :2@N1_:1@N4 56730 0.679 6.06 0.638 57 :2@C2_:1@C4 56679 0.679 6.11 0.659 58 :2@C4_:1@C5 55877 0.669 6.29 0.477 59 :2@N3_:1@C5 48562 0.582 6.34 0.51 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0042 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 83496 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 83496 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 83496 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 83496 COM "COM" (double, distance), size is 83496 v_base2 "v_base2" (vector), size is 83496 v_base1 "v_base1" (vector), size is 83496 normalangle "normalangle" (double), size is 83496 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: 0.6087 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.