CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 18:33:39 | Available memory: 50886.6 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.c5] Reading '../ctraj.c5' 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, 8913 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 8913 of 8913) Coordinate processing will occur on 8913 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.c5 (1-8913, 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 63 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' 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@N9' 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@N9' 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@C5' Atom ':1@C5' to ':2@C6' 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@C5' Atom ':1@C6' to ':2@C6' 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@C5' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@N3' Atom ':1@N6' to ':2@C4' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N3' to ':2@N9' 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@C5' Atom ':1@C4' to ':2@C6' 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 8913 frames and processed 8913 frames. TIME: Trajectory processing: 0.0578 s TIME: Avg. throughput= 154193.4814 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 59.4866 63 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@N3 8913 1 4.04 0.521 2 :1@N3_:2@N3 8910 1 3.95 0.618 3 :1@C4_:2@C2 8902 0.999 3.94 0.632 4 :1@C6_:2@N3 8900 0.999 4.49 0.606 5 :1@C5_:2@N3 8899 0.998 4.33 0.597 6 :1@N3_:2@C4 8896 0.998 4.46 0.715 7 :1@C5_:2@C2 8885 0.997 3.95 0.672 8 :1@N9_:2@N3 8884 0.997 4.5 0.598 9 :1@N3_:2@N9 8882 0.997 4.9 0.677 10 :1@C2_:2@N3 8877 0.996 4.08 0.746 11 :1@N3_:2@C2 8864 0.995 4.24 0.739 12 :1@N1_:2@N3 8855 0.993 4.37 0.676 13 :1@N9_:2@C2 8854 0.993 4.21 0.622 14 :1@C2_:2@N9 8852 0.993 4.52 0.78 15 :1@C4_:2@C4 8849 0.993 4.69 0.64 16 :1@C6_:2@C4 8833 0.991 4.6 0.752 17 :1@N1_:2@N9 8827 0.99 4.74 0.769 18 :1@N7_:2@C2 8817 0.989 4.26 0.75 19 :1@C2_:2@C4 8810 0.988 4.21 0.812 20 :1@N1_:2@C4 8809 0.988 4.32 0.786 21 :1@C6_:2@C2 8794 0.987 4.24 0.707 22 :1@C4_:2@N1 8770 0.984 4.47 0.712 23 :1@C5_:2@N1 8767 0.984 4.1 0.796 24 :1@C8_:2@C2 8763 0.983 4.34 0.744 25 :1@C5_:2@C4 8737 0.98 4.77 0.705 26 :1@N7_:2@N3 8736 0.98 4.91 0.728 27 :1@N6_:2@N3 8714 0.978 5.21 0.604 28 :1@N7_:2@N1 8673 0.973 4.25 0.822 29 :1@C8_:2@N3 8673 0.973 4.94 0.726 30 :1@N9_:2@N1 8671 0.973 4.79 0.63 31 :1@C2_:2@C2 8641 0.969 4.39 0.797 32 :1@N1_:2@C2 8590 0.964 4.43 0.741 33 :1@N6_:2@C2 8583 0.963 4.81 0.662 34 :1@C4_:2@N9 8580 0.963 5.38 0.587 35 :1@C6_:2@N1 8571 0.962 4.17 0.794 36 :1@C8_:2@N1 8547 0.959 4.6 0.741 37 :1@C5_:2@C6 8534 0.957 4.56 0.868 38 :1@N9_:2@C4 8515 0.955 5.33 0.579 39 :1@N3_:2@N1 8513 0.955 4.88 0.703 40 :1@C4_:2@C5 8510 0.955 5.16 0.731 41 :1@N6_:2@C4 8506 0.954 5.1 0.724 42 :1@C4_:2@C6 8492 0.953 5.02 0.738 43 :1@C6_:2@C5 8482 0.952 4.5 0.943 44 :1@C6_:2@N9 8469 0.95 5.22 0.683 45 :1@C6_:2@C6 8443 0.947 4.27 0.946 46 :1@N6_:2@N1 8436 0.946 4.41 0.788 47 :1@C5_:2@C5 8371 0.939 4.88 0.804 48 :1@N7_:2@C6 8168 0.916 4.83 0.796 49 :1@N9_:2@C6 8141 0.913 5.54 0.591 50 :1@N6_:2@C5 8090 0.908 4.62 0.887 51 :1@C5_:2@N9 8065 0.905 5.51 0.6 52 :1@N7_:2@C4 8016 0.899 5.37 0.696 53 :1@C8_:2@C6 7904 0.887 5.36 0.684 54 :1@C8_:2@C4 7828 0.878 5.62 0.656 55 :1@N9_:2@C5 7810 0.876 5.79 0.551 56 :1@N6_:2@N9 7737 0.868 5.66 0.633 57 :1@N7_:2@C5 7707 0.865 5.38 0.73 58 :1@N7_:2@N6 7687 0.862 5.15 0.773 59 :1@N9_:2@N9 7569 0.849 6.05 0.472 60 :1@C8_:2@C5 7347 0.824 5.85 0.658 61 :1@C8_:2@N6 7170 0.804 5.84 0.642 62 :1@N7_:2@N9 6269 0.703 6.14 0.631 63 :1@C8_:2@N9 5297 0.594 6.32 0.582 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0005 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 8913 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 8913 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 8913 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 8913 COM "COM" (double, distance), size is 8913 v_base1 "v_base1" (vector), size is 8913 v_base2 "v_base2" (vector), size is 8913 normalangle "normalangle" (double), size is 8913 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: 0.1053 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.