CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:18:23 | Available memory: 1.222 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,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_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,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 (1 total): 0: [traj] noWAt.topo.hmr, 63 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 88557 of 88557) Coordinate processing will occur on 88557 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*](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] 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] Mask [:1@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-88557, 1) ----- 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' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 88557 frames and processed 88557 frames. TIME: Avg. throughput= 127586.0976 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 50.1737 59 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 84687 0.956 4.64 0.689 2 :2@N7_:1@N1 83955 0.948 4.99 0.735 3 :2@C6_:1@N1 83846 0.947 4.25 0.73 4 :2@N6_:1@N1 83229 0.94 4.15 0.766 5 :2@C4_:1@N1 83203 0.94 5.19 0.593 6 :2@N1_:1@N1 82264 0.929 4.49 0.743 7 :2@C6_:1@C6 81964 0.926 4.52 0.787 8 :2@N6_:1@C2 81717 0.923 4.27 0.889 9 :2@N6_:1@C6 81685 0.922 4.32 0.872 10 :2@C6_:1@C2 81658 0.922 4.57 0.734 11 :2@C6_:1@O2 81642 0.922 4.76 0.81 12 :2@C5_:1@C6 81575 0.921 5.02 0.71 13 :2@C5_:1@C2 81511 0.92 5.08 0.675 14 :2@C5_:1@O2 81424 0.919 5.13 0.766 15 :2@N6_:1@O2 81311 0.918 4.52 1.05 16 :2@C2_:1@N1 81291 0.918 5.03 0.741 17 :2@C8_:1@N1 81205 0.917 5.64 0.639 18 :2@N3_:1@N1 80924 0.914 5.42 0.638 19 :2@N9_:1@N1 80664 0.911 5.82 0.524 20 :2@N1_:1@C6 80507 0.909 4.69 0.781 21 :2@N1_:1@C2 80001 0.903 4.8 0.825 22 :2@N7_:1@C6 79439 0.897 5.42 0.753 23 :2@N1_:1@O2 79003 0.892 4.98 0.945 24 :2@N7_:1@C2 78943 0.891 5.37 0.848 25 :2@C4_:1@C6 78937 0.891 5.6 0.588 26 :2@C2_:1@C6 78688 0.889 5.29 0.734 27 :2@N6_:1@N3 78479 0.886 4.59 0.851 28 :2@C4_:1@C2 78320 0.884 5.72 0.549 29 :2@N6_:1@C5 78302 0.884 4.6 0.897 30 :2@C4_:1@O2 78178 0.883 5.72 0.564 31 :2@C6_:1@N3 77510 0.875 5.13 0.685 32 :2@C6_:1@C5 77397 0.874 5.06 0.75 33 :2@N6_:1@C4 77335 0.873 4.74 0.822 34 :2@C2_:1@C2 77138 0.871 5.43 0.857 35 :2@N7_:1@O2 76774 0.867 5.26 1.09 36 :2@N1_:1@C5 76470 0.864 5.19 0.764 37 :2@N3_:1@C6 76385 0.863 5.77 0.615 38 :2@N1_:1@N3 75871 0.857 5.3 0.79 39 :2@C6_:1@C4 75543 0.853 5.33 0.681 40 :2@C2_:1@O2 74125 0.837 5.46 1.02 41 :2@N1_:1@C4 74035 0.836 5.46 0.728 42 :2@N3_:1@C2 73621 0.831 5.9 0.691 43 :2@C5_:1@C5 72964 0.824 5.72 0.645 44 :2@C5_:1@N3 72952 0.824 5.79 0.583 45 :2@N3_:1@O2 71249 0.805 5.87 0.791 46 :2@N6_:1@N4 71039 0.802 5.38 0.765 47 :2@C8_:1@C6 70808 0.8 6.05 0.616 48 :2@C2_:1@C5 68628 0.775 5.86 0.685 49 :2@N9_:1@C6 68322 0.772 6.22 0.498 50 :2@C5_:1@C4 66761 0.754 6.02 0.557 51 :2@C8_:1@C2 66040 0.746 5.99 0.68 52 :2@C2_:1@N3 63776 0.72 5.94 0.781 53 :2@C8_:1@O2 62406 0.705 5.75 0.854 54 :2@C6_:1@N4 62016 0.7 6.02 0.582 55 :2@N7_:1@N3 61441 0.694 5.97 0.682 56 :2@C4_:1@C5 57942 0.654 6.28 0.481 57 :2@C2_:1@C4 57890 0.654 6.1 0.666 58 :2@N1_:1@N4 57844 0.653 6.06 0.638 59 :2@N3_:1@C5 50400 0.569 6.33 0.524 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 88557, 'v_base2' size 88557, output size 88557 TIME: Analyses took 0.0062 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 88557 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 88557 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 88557 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 88557 COM "COM" (double, distance), size is 88557 v_base2 "v_base2" (vector, vector), size is 88557 v_base1 "v_base1" (vector, vector), size is 88557 normalangle "normalangle" (double), size is 88557 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0009 s ( 0.13%) TIME: Trajectory Process : 0.6941 s ( 98.96%) TIME: Action Post : 0.0001 s ( 0.02%) TIME: Analysis : 0.0062 s ( 0.88%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7014 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: 0.9448 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.