CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/17/15 18:33:35 | Available memory: 50903.2 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.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,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, 30190 frames INPUT TRAJECTORIES: 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 30190 of 30190) Coordinate processing will occur on 30190 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.c1 (1-30190, 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 71 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@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@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@N7' to ':2@N3' Atom ':1@N7' to ':2@C4' 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@C5' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@N6' Atom ':1@N6' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' 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@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 30190 frames and processed 30190 frames. TIME: Trajectory processing: 0.1753 s TIME: Avg. throughput= 172241.6518 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 53.2028 71 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@N7 28473 0.943 4.95 0.817 2 :1@N9_:2@C5 28246 0.936 4.66 0.697 3 :1@N9_:2@C6 27941 0.926 4.34 0.685 4 :1@N9_:2@N6 27927 0.925 4.23 0.74 5 :1@N9_:2@C4 27570 0.913 5.26 0.562 6 :1@C8_:2@N6 27376 0.907 3.98 0.811 7 :1@C4_:2@C6 27292 0.904 4.94 0.71 8 :1@N9_:2@C8 27268 0.903 5.58 0.722 9 :1@N9_:2@N1 27214 0.901 4.68 0.647 10 :1@C4_:2@N6 27187 0.901 4.81 0.807 11 :1@C8_:2@C6 27177 0.9 4.42 0.703 12 :1@C8_:2@C5 27118 0.898 4.9 0.709 13 :1@C4_:2@C5 27089 0.897 5.42 0.685 14 :1@N3_:2@C6 27018 0.895 5.47 0.767 15 :1@C4_:2@N1 26836 0.889 5.03 0.636 16 :1@C8_:2@N7 26820 0.888 5.08 0.897 17 :1@N9_:2@N9 26744 0.886 5.83 0.568 18 :1@N9_:2@C2 26697 0.884 5.25 0.601 19 :1@N3_:2@N1 26670 0.883 5.37 0.743 20 :1@N9_:2@N3 26580 0.88 5.59 0.505 21 :1@N7_:2@N6 26574 0.88 4.47 0.775 22 :1@C8_:2@N1 26508 0.878 4.86 0.734 23 :1@N3_:2@C5 26367 0.873 5.86 0.653 24 :1@C5_:2@N6 26209 0.868 4.91 0.859 25 :1@N7_:2@C6 26139 0.866 5.05 0.637 26 :1@N3_:2@N6 26098 0.864 5.51 0.849 27 :1@C4_:2@C2 26096 0.864 5.54 0.58 28 :1@C4_:2@C4 26037 0.862 5.9 0.534 29 :1@C5_:2@C6 25965 0.86 5.3 0.699 30 :1@C5_:2@N1 25810 0.855 5.4 0.602 31 :1@N3_:2@C2 25736 0.852 5.62 0.651 32 :1@N7_:2@N1 25730 0.852 5.33 0.636 33 :1@C8_:2@C4 25639 0.849 5.69 0.549 34 :1@N3_:2@C4 25433 0.842 6.1 0.533 35 :1@C8_:2@C2 25354 0.84 5.64 0.662 36 :1@C4_:2@N3 25125 0.832 6 0.484 37 :1@C4_:2@N7 25062 0.83 5.79 0.736 38 :1@N7_:2@C5 24779 0.821 5.68 0.665 39 :1@N3_:2@N3 24682 0.818 6.01 0.533 40 :1@C8_:2@C8 23837 0.79 5.83 0.81 41 :1@C5_:2@C5 23790 0.788 5.91 0.685 42 :1@C8_:2@N3 23763 0.787 6.07 0.497 43 :1@C5_:2@C2 23432 0.776 6.04 0.514 44 :1@C2_:2@N1 22540 0.747 5.85 0.789 45 :1@C6_:2@N6 22463 0.744 5.64 0.968 46 :1@N7_:2@C2 22330 0.74 6.09 0.55 47 :1@C6_:2@N1 22188 0.735 5.99 0.611 48 :1@N7_:2@N7 21729 0.72 5.84 0.88 49 :1@C8_:2@N9 21497 0.712 6.2 0.592 50 :1@N3_:2@N7 21075 0.698 6.21 0.597 51 :1@C6_:2@C6 20650 0.684 6.01 0.743 52 :1@C2_:2@C6 20245 0.671 6 0.816 53 :1@N7_:2@C4 18944 0.627 6.35 0.453 54 :1@C4_:2@C8 18806 0.623 6.25 0.601 55 :1@C2_:2@N6 18736 0.621 5.85 0.965 56 :1@C4_:2@N9 18697 0.619 6.4 0.471 57 :1@N1_:2@N1 18156 0.601 6.06 0.704 58 :1@C5_:2@C4 17368 0.575 6.4 0.463 59 :1@C5_:2@N7 17351 0.575 6.05 0.806 60 :1@C5_:2@N3 16077 0.533 6.49 0.353 61 :1@N6_:2@N6 15646 0.518 5.88 0.917 62 :1@N1_:2@N6 15525 0.514 5.8 1.02 63 :1@N3_:2@N9 15246 0.505 6.52 0.398 64 :1@N7_:2@N3 14566 0.482 6.52 0.354 65 :1@N1_:2@C6 13988 0.463 6.05 0.794 66 :1@N6_:2@N1 12896 0.427 6.37 0.471 67 :1@N3_:2@C8 12834 0.425 6.45 0.452 68 :1@C2_:2@C5 12371 0.41 6.25 0.648 69 :1@N6_:2@C6 9951 0.33 6.19 0.627 70 :1@C6_:2@C5 9319 0.309 6.2 0.641 71 :1@C2_:2@N7 5590 0.185 6.3 0.517 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0014 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 30190 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 30190 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 30190 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 30190 COM "COM" (double, distance), size is 30190 v_base1 "v_base1" (vector), size is 30190 v_base2 "v_base2" (vector), size is 30190 normalangle "normalangle" (double), size is 30190 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: 0.2624 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.