CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 18:33:37 | Available memory: 50894.2 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.c3] Reading '../ctraj.c3' 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, 13239 frames INPUT TRAJECTORIES: 0: 'ctraj.c3' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 13239 of 13239) Coordinate processing will occur on 13239 frames. TIME: Run Initialization took 0.0000 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.c3 (1-13239, 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 67 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@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' 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@C2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' 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@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@C4' 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@N6' to ':2@N6' 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@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@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@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@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 13239 frames and processed 13239 frames. TIME: Trajectory processing: 0.0819 s TIME: Avg. throughput= 161622.6973 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 58.5389 67 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N1 13206 0.998 4.11 0.618 2 :1@N9_:2@C2 13180 0.996 4.54 0.626 3 :1@N9_:2@C6 13172 0.995 4.16 0.626 4 :1@N9_:2@N3 13147 0.993 5.04 0.631 5 :1@C8_:2@N1 13120 0.991 4.06 0.76 6 :1@N9_:2@C4 13094 0.989 5.05 0.567 7 :1@C4_:2@C6 13066 0.987 4.68 0.736 8 :1@N9_:2@N6 13054 0.986 4.24 0.705 9 :1@N9_:2@C5 13053 0.986 4.67 0.552 10 :1@C4_:2@N1 13050 0.986 4.87 0.782 11 :1@C8_:2@C2 13043 0.985 4.63 0.783 12 :1@C8_:2@C6 12974 0.98 4.28 0.705 13 :1@C4_:2@N6 12944 0.978 4.5 0.762 14 :1@N3_:2@C6 12901 0.974 5.17 0.815 15 :1@C8_:2@N6 12877 0.973 4.16 0.881 16 :1@C4_:2@C5 12869 0.972 5.13 0.628 17 :1@C4_:2@C2 12854 0.971 5.44 0.776 18 :1@N3_:2@C5 12806 0.967 5.38 0.707 19 :1@N7_:2@N1 12784 0.966 4.75 0.833 20 :1@N3_:2@N1 12710 0.96 5.55 0.801 21 :1@C8_:2@N3 12706 0.96 5.35 0.761 22 :1@N3_:2@N6 12697 0.959 5.03 0.875 23 :1@C4_:2@C4 12670 0.957 5.69 0.613 24 :1@C8_:2@C5 12654 0.956 5.07 0.535 25 :1@N7_:2@N6 12647 0.955 4.44 0.816 26 :1@C5_:2@N6 12645 0.955 4.6 0.809 27 :1@N7_:2@C6 12619 0.953 4.85 0.671 28 :1@N9_:2@N7 12601 0.952 5.33 0.479 29 :1@C5_:2@C6 12577 0.95 5.02 0.754 30 :1@C5_:2@N1 12510 0.945 5.14 0.909 31 :1@C8_:2@C4 12504 0.944 5.49 0.579 32 :1@N9_:2@N9 12478 0.943 5.83 0.498 33 :1@N3_:2@C4 12430 0.939 5.93 0.596 34 :1@C4_:2@N3 12392 0.936 5.87 0.69 35 :1@C4_:2@N7 12351 0.933 5.54 0.532 36 :1@N3_:2@N7 12293 0.929 5.53 0.645 37 :1@N9_:2@C8 12210 0.922 5.92 0.436 38 :1@N7_:2@C5 12040 0.909 5.7 0.501 39 :1@C8_:2@N7 12004 0.907 5.85 0.484 40 :1@N7_:2@C2 11998 0.906 5.4 0.896 41 :1@C5_:2@C5 11972 0.904 5.68 0.571 42 :1@N3_:2@C2 11903 0.899 6.02 0.699 43 :1@C6_:2@N6 11646 0.88 5.17 0.866 44 :1@C2_:2@N6 11215 0.847 5.36 1.01 45 :1@C4_:2@C8 11212 0.847 6.18 0.431 46 :1@N3_:2@C8 11187 0.845 6.07 0.496 47 :1@N3_:2@N3 11163 0.843 6.24 0.588 48 :1@C5_:2@N7 10987 0.83 6.11 0.445 49 :1@C5_:2@C2 10915 0.824 5.73 0.905 50 :1@C4_:2@N9 10834 0.818 6.29 0.466 51 :1@C6_:2@C6 10780 0.814 5.69 0.787 52 :1@C2_:2@C6 10780 0.814 5.7 0.889 53 :1@N3_:2@N9 10565 0.798 6.3 0.449 54 :1@N1_:2@N6 10511 0.794 5.43 0.972 55 :1@C2_:2@C5 10377 0.784 5.97 0.686 56 :1@N7_:2@N7 10339 0.781 6.29 0.41 57 :1@N6_:2@N6 10263 0.775 5.64 0.764 58 :1@C2_:2@N7 10131 0.765 6 0.583 59 :1@C5_:2@C4 9773 0.738 6.21 0.584 60 :1@N1_:2@C6 8874 0.67 5.85 0.848 61 :1@C6_:2@C5 8701 0.657 6.22 0.541 62 :1@C2_:2@N1 8273 0.625 5.92 0.916 63 :1@C6_:2@N7 7237 0.547 6.46 0.379 64 :1@N1_:2@C5 7024 0.531 6.22 0.584 65 :1@N1_:2@N7 6985 0.528 6.38 0.439 66 :1@C2_:2@C8 6546 0.494 6.47 0.385 67 :1@C2_:2@C4 5874 0.444 6.35 0.547 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0007 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 13239 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 13239 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 13239 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 13239 COM "COM" (double, distance), size is 13239 v_base1 "v_base1" (vector), size is 13239 v_base2 "v_base2" (vector), size is 13239 normalangle "normalangle" (double), size is 13239 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: 0.1374 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.