CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:43:59 | Available memory: 3.941 GB INPUT: Reading input from '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-] Warning: Action specified before trajin/ensemble. Assuming trajin. 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*). Best-fit RMSD will be calculated, coords will be rotated and translated. [nativecontacts :2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,C2,N3,C4,C5,C6,O6,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_00002 Saving minimum observed distances in set 'Contacts_00002[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,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 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,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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 (1 total): 0: [traj] noWAt.topo.hmr, 64 atoms, 2 res, box: Orthogonal, 1 mol INPUT TRAJECTORIES (1 total): 0: 'ctraj.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 18419 of 18419) Coordinate processing will occur on 18419 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'noWAt.topo.hmr' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology 'noWAt.topo.hmr' Warning: Setup incomplete for [strip]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](40) Reference mask: [:1,2&!@H*](40) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :1@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,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,N2,H21,H22,N7,C8,H8,N9,O6 :1@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (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,N2,N7,C8,N9,O6 corrplane] Mask [:2@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base1 :1@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-18419, 1) ----- Using first frame to determine native contacts. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 74 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@C2' Atom ':2@N9' to ':1@O2' 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@C5' Atom ':2@N7' to ':1@C4' 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@O6' to ':1@N1' Atom ':2@O6' to ':1@C6' Atom ':2@O6' to ':1@C5' Atom ':2@O6' to ':1@C4' Atom ':2@O6' to ':1@N4' Atom ':2@O6' to ':1@N3' Atom ':2@O6' to ':1@C2' Atom ':2@O6' 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@N4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N2' to ':1@N1' Atom ':2@N2' to ':1@C6' Atom ':2@N2' to ':1@C5' Atom ':2@N2' to ':1@C4' Atom ':2@N2' to ':1@N3' Atom ':2@N2' to ':1@C2' Atom ':2@N3' to ':1@N1' Atom ':2@N3' to ':1@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@N3' 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@C4' Atom ':2@C4' to ':1@N3' Atom ':2@C4' to ':1@C2' Atom ':2@C4' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 18419 frames and processed 18419 frames. TIME: Avg. throughput= 70227.8143 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 59.4384 74 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 17688 0.96 4.79 0.649 2 :2@C6_:1@N1 17567 0.954 4.29 0.687 3 :2@C4_:1@N1 17495 0.95 5.22 0.566 4 :2@O6_:1@N1 17472 0.949 4.32 0.781 5 :2@N1_:1@N1 17352 0.942 4.3 0.694 6 :2@N7_:1@N1 17303 0.939 5.33 0.736 7 :2@C6_:1@C6 17269 0.938 4.5 0.759 8 :2@C6_:1@C2 17252 0.937 4.7 0.756 9 :2@C6_:1@O2 17189 0.933 4.93 0.874 10 :2@O6_:1@C6 17188 0.933 4.36 0.896 11 :2@O6_:1@C2 17184 0.933 4.58 0.935 12 :2@C2_:1@N1 17184 0.933 4.76 0.719 13 :2@C5_:1@C6 17177 0.933 5.1 0.69 14 :2@N3_:1@N1 17165 0.932 5.26 0.637 15 :2@N1_:1@C6 17125 0.93 4.57 0.749 16 :2@C5_:1@C2 17080 0.927 5.33 0.654 17 :2@N1_:1@C2 16983 0.922 4.6 0.805 18 :2@C5_:1@O2 16880 0.916 5.44 0.728 19 :2@N1_:1@O2 16873 0.916 4.76 1 20 :2@C2_:1@C6 16835 0.914 5.15 0.748 21 :2@O6_:1@O2 16768 0.91 4.87 1.08 22 :2@C4_:1@C6 16747 0.909 5.62 0.578 23 :2@N9_:1@N1 16655 0.904 5.95 0.519 24 :2@C2_:1@C2 16559 0.899 5.1 0.836 25 :2@O6_:1@C5 16554 0.899 4.7 0.891 26 :2@C4_:1@C2 16542 0.898 5.78 0.55 27 :2@C6_:1@C5 16530 0.897 5.08 0.737 28 :2@O6_:1@N3 16491 0.895 4.92 0.925 29 :2@C6_:1@N3 16480 0.895 5.26 0.729 30 :2@N3_:1@C6 16480 0.895 5.7 0.652 31 :2@N2_:1@N1 16445 0.893 5.12 0.82 32 :2@N1_:1@C5 16440 0.893 5.11 0.765 33 :2@C4_:1@O2 16399 0.89 5.78 0.57 34 :2@O6_:1@C4 16295 0.885 4.98 0.848 35 :2@N1_:1@N3 16275 0.884 5.15 0.755 36 :2@N7_:1@C6 16258 0.883 5.57 0.749 37 :2@C2_:1@O2 16196 0.879 5.08 1.03 38 :2@C8_:1@N1 16114 0.875 5.89 0.624 39 :2@C6_:1@C4 16046 0.871 5.41 0.674 40 :2@N3_:1@C2 15979 0.868 5.7 0.697 41 :2@N1_:1@C4 15928 0.865 5.36 0.698 42 :2@N2_:1@C6 15806 0.858 5.48 0.854 43 :2@N3_:1@O2 15666 0.851 5.63 0.806 44 :2@C5_:1@C5 15282 0.83 5.81 0.608 45 :2@N7_:1@C2 15185 0.824 5.78 0.772 46 :2@C2_:1@C5 15162 0.823 5.76 0.76 47 :2@N2_:1@C2 15006 0.815 5.18 0.988 48 :2@C5_:1@N3 14631 0.794 5.99 0.572 49 :2@C2_:1@N3 14612 0.793 5.7 0.741 50 :2@O6_:1@N4 14387 0.781 5.57 0.754 51 :2@N7_:1@O2 13911 0.755 5.72 0.931 52 :2@N9_:1@C6 13847 0.752 6.27 0.487 53 :2@C8_:1@C6 13717 0.745 6.16 0.594 54 :2@C2_:1@C4 13658 0.742 5.97 0.703 55 :2@C5_:1@C4 13280 0.721 6.15 0.531 56 :2@N1_:1@N4 13128 0.713 6.03 0.629 57 :2@C6_:1@N4 12868 0.699 6.08 0.573 58 :2@N2_:1@N3 12631 0.686 5.61 0.881 59 :2@N2_:1@C5 12552 0.681 5.81 0.885 60 :2@N9_:1@O2 12298 0.668 6.33 0.517 61 :2@C4_:1@C5 12275 0.666 6.32 0.494 62 :2@N9_:1@C2 12027 0.653 6.39 0.474 63 :2@N7_:1@C5 11876 0.645 6.12 0.647 64 :2@N2_:1@C4 11451 0.622 5.93 0.859 65 :2@N3_:1@C5 11027 0.599 6.26 0.62 66 :2@C8_:1@C2 10982 0.596 6.23 0.626 67 :2@C4_:1@N3 10824 0.588 6.4 0.462 68 :2@N3_:1@N3 10583 0.575 6.25 0.624 69 :2@C8_:1@O2 10319 0.56 6.09 0.762 70 :2@N7_:1@N3 9548 0.518 6.18 0.629 71 :2@N7_:1@C4 7798 0.423 6.33 0.571 72 :2@C4_:1@C4 7099 0.385 6.49 0.459 73 :2@N3_:1@C4 6786 0.368 6.35 0.634 74 :2@C2_:1@N4 6131 0.333 6.26 0.679 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 18419, 'v_base2' size 18419, output size 18419 TIME: Analyses took 0.0013 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 18419 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 18419 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 18419 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 18419 COM "COM" (double, distance), size is 18419 v_base2 "v_base2" (vector, vector), size is 18419 v_base1 "v_base1" (vector, vector), size is 18419 normalangle "normalangle" (double), size is 18419 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.2623 s ( 99.43%) TIME: Action Post : 0.0001 s ( 0.05%) TIME: Analysis : 0.0013 s ( 0.49%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2638 s ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00002[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00002[mindist] COM normalangle TIME: Total execution time: 0.3483 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.