CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:18:15 | Available memory: 1.229 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 93378 of 93378) Coordinate processing will occur on 93378 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 (1-93378, 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 93378 frames and processed 93378 frames. TIME: Avg. throughput= 126667.8242 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 49.7801 59 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 90522 0.969 4.7 0.731 2 :2@N7_:1@N1 90163 0.966 5.03 0.735 3 :2@C6_:1@N1 88972 0.953 4.32 0.782 4 :2@N6_:1@N1 88642 0.949 4.22 0.806 5 :2@C4_:1@N1 87630 0.938 5.24 0.636 6 :2@N6_:1@C2 87098 0.933 4.35 0.936 7 :2@C8_:1@N1 86780 0.929 5.66 0.639 8 :2@C5_:1@C2 86754 0.929 5.14 0.712 9 :2@N6_:1@C6 86644 0.928 4.34 0.893 10 :2@C6_:1@C2 86585 0.927 4.64 0.793 11 :2@C6_:1@C6 86470 0.926 4.55 0.81 12 :2@N1_:1@N1 86206 0.923 4.54 0.796 13 :2@C5_:1@C6 86135 0.922 5.04 0.724 14 :2@N6_:1@O2 86043 0.921 4.57 1.08 15 :2@C6_:1@O2 85568 0.916 4.78 0.832 16 :2@C5_:1@O2 85277 0.913 5.15 0.784 17 :2@N7_:1@C6 85004 0.91 5.42 0.762 18 :2@N9_:1@N1 84712 0.907 5.86 0.535 19 :2@N7_:1@C2 84511 0.905 5.41 0.854 20 :2@N1_:1@C6 84088 0.901 4.72 0.794 21 :2@C2_:1@N1 83426 0.893 5.05 0.763 22 :2@N6_:1@N3 83215 0.891 4.65 0.881 23 :2@N6_:1@C5 82961 0.888 4.61 0.912 24 :2@N1_:1@C2 82861 0.887 4.82 0.846 25 :2@N3_:1@N1 82526 0.884 5.44 0.651 26 :2@C4_:1@C6 82082 0.879 5.61 0.588 27 :2@N6_:1@C4 81887 0.877 4.78 0.832 28 :2@N1_:1@O2 81715 0.875 4.97 0.945 29 :2@C2_:1@C6 81411 0.872 5.31 0.735 30 :2@C6_:1@C5 81263 0.87 5.06 0.757 31 :2@C6_:1@N3 81192 0.869 5.17 0.712 32 :2@C4_:1@O2 81094 0.868 5.71 0.571 33 :2@N7_:1@O2 80944 0.867 5.27 1.11 34 :2@C4_:1@C2 80770 0.865 5.74 0.556 35 :2@N1_:1@C5 79683 0.853 5.2 0.77 36 :2@C6_:1@C4 79174 0.848 5.36 0.695 37 :2@N3_:1@C6 78677 0.843 5.78 0.611 38 :2@C2_:1@C2 78667 0.842 5.41 0.864 39 :2@N1_:1@N3 78017 0.835 5.3 0.803 40 :2@N1_:1@C4 76512 0.819 5.47 0.747 41 :2@C5_:1@C5 76512 0.819 5.71 0.648 42 :2@C2_:1@O2 76290 0.817 5.44 1.02 43 :2@C5_:1@N3 76122 0.815 5.81 0.593 44 :2@C8_:1@C6 75512 0.809 6.05 0.622 45 :2@N6_:1@N4 74873 0.802 5.4 0.766 46 :2@N3_:1@C2 74775 0.801 5.9 0.693 47 :2@N3_:1@O2 73507 0.787 5.86 0.793 48 :2@N9_:1@C6 70883 0.759 6.22 0.496 49 :2@C2_:1@C5 70793 0.758 5.87 0.682 50 :2@C5_:1@C4 69483 0.744 6.04 0.558 51 :2@C8_:1@C2 69356 0.743 5.99 0.688 52 :2@N7_:1@N3 65005 0.696 5.98 0.68 53 :2@C2_:1@N3 65002 0.696 5.92 0.786 54 :2@C8_:1@O2 64807 0.694 5.72 0.877 55 :2@C6_:1@N4 64125 0.687 6.02 0.585 56 :2@C4_:1@C5 60077 0.643 6.28 0.478 57 :2@N1_:1@N4 59080 0.633 6.05 0.648 58 :2@C2_:1@C4 58778 0.629 6.09 0.668 59 :2@N3_:1@C5 51507 0.552 6.33 0.512 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 93378, 'v_base2' size 93378, output size 93378 TIME: Analyses took 0.0068 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 93378 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 93378 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 93378 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 93378 COM "COM" (double, distance), size is 93378 v_base2 "v_base2" (vector, vector), size is 93378 v_base1 "v_base1" (vector, vector), size is 93378 normalangle "normalangle" (double), size is 93378 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0010 s ( 0.14%) TIME: Trajectory Process : 0.7372 s ( 98.93%) TIME: Action Post : 0.0001 s ( 0.02%) TIME: Analysis : 0.0068 s ( 0.91%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7452 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: 1.4730 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.