CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/01/16 18:20:54 | Available memory: 1.234 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@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 :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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 24626 of 24626) Coordinate processing will occur on 24626 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base2 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [vector v_base1 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-24626, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 68 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N4' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N4' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@N4' Atom ':1@C6' to ':2@N3' Atom ':1@O6' to ':2@N4' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@N4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@N4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C4' Atom ':1@N2' to ':2@N4' Atom ':1@N2' to ':2@N3' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@N4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 24626 frames and processed 24626 frames. TIME: Avg. throughput= 118146.5774 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 61.7165 68 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N1 24229 0.984 4.54 0.702 2 :1@N3_:2@C6 24024 0.976 4.34 0.767 3 :1@C2_:2@N1 23925 0.972 4.52 0.785 4 :1@C4_:2@C6 23809 0.967 4.52 0.673 5 :1@C4_:2@N1 23775 0.965 4.88 0.583 6 :1@N9_:2@C6 23659 0.961 4.82 0.62 7 :1@C2_:2@C6 23603 0.958 4.63 0.835 8 :1@N3_:2@C2 23529 0.955 4.69 0.729 9 :1@C2_:2@C2 23413 0.951 4.39 0.85 10 :1@N3_:2@C5 23363 0.949 4.28 0.796 11 :1@N9_:2@N1 23338 0.948 5.41 0.603 12 :1@N2_:2@N1 23314 0.947 4.59 0.956 13 :1@C4_:2@C5 23246 0.944 4.19 0.747 14 :1@N1_:2@N1 23229 0.943 4.87 0.628 15 :1@N9_:2@C5 23161 0.941 4.42 0.684 16 :1@C4_:2@C2 23150 0.94 4.94 0.69 17 :1@C5_:2@N1 22972 0.933 5.2 0.617 18 :1@N1_:2@C2 22944 0.932 4.42 0.744 19 :1@C5_:2@C6 22926 0.931 4.97 0.637 20 :1@N3_:2@C4 22896 0.93 4.44 0.72 21 :1@C2_:2@O2 22884 0.929 4.73 0.852 22 :1@N3_:2@N3 22875 0.929 4.64 0.703 23 :1@C4_:2@C4 22855 0.928 4.28 0.699 24 :1@N2_:2@C6 22847 0.928 4.91 0.904 25 :1@C4_:2@N3 22765 0.924 4.67 0.723 26 :1@N2_:2@C2 22720 0.923 4.48 1.01 27 :1@C2_:2@N3 22667 0.92 4.32 0.823 28 :1@C5_:2@C5 22651 0.92 4.44 0.769 29 :1@N9_:2@C4 22611 0.918 4.73 0.719 30 :1@N3_:2@O2 22610 0.918 5.24 0.731 31 :1@C2_:2@C5 22580 0.917 4.53 0.86 32 :1@C5_:2@C2 22572 0.917 4.97 0.764 33 :1@N1_:2@C6 22538 0.915 5.04 0.705 34 :1@C8_:2@C5 22514 0.914 4.76 0.758 35 :1@C8_:2@C6 22507 0.914 5.36 0.672 36 :1@N1_:2@N3 22497 0.914 4.14 0.822 37 :1@C5_:2@C4 22439 0.911 4.18 0.762 38 :1@C5_:2@N3 22390 0.909 4.48 0.798 39 :1@C2_:2@C4 22357 0.908 4.37 0.832 40 :1@C6_:2@N3 22312 0.906 4.23 0.764 41 :1@C4_:2@N4 22198 0.901 4.51 0.7 42 :1@N1_:2@C4 22155 0.9 4.29 0.858 43 :1@C6_:2@C4 22135 0.899 4.23 0.788 44 :1@N9_:2@C2 22047 0.895 5.62 0.722 45 :1@N3_:2@N4 22021 0.894 4.88 0.716 46 :1@N9_:2@N3 22017 0.894 5.31 0.779 47 :1@N7_:2@C6 22005 0.894 5.48 0.659 48 :1@N2_:2@O2 22000 0.893 4.59 1 49 :1@C6_:2@C5 21979 0.893 4.77 0.769 50 :1@N1_:2@C5 21976 0.892 4.76 0.83 51 :1@N7_:2@C5 21963 0.892 4.8 0.717 52 :1@C8_:2@C4 21900 0.889 4.83 0.857 53 :1@N9_:2@N4 21879 0.888 4.85 0.742 54 :1@C4_:2@O2 21877 0.888 5.58 0.75 55 :1@C5_:2@N4 21873 0.888 4.14 0.805 56 :1@N7_:2@C4 21831 0.887 4.57 0.816 57 :1@N2_:2@N3 21806 0.885 4.63 0.923 58 :1@C6_:2@N4 21650 0.879 4.18 0.885 59 :1@N7_:2@N4 21358 0.867 4.28 0.911 60 :1@N2_:2@C5 21349 0.867 4.97 0.862 61 :1@N1_:2@N4 21306 0.865 4.47 0.906 62 :1@C2_:2@N4 21272 0.864 4.75 0.843 63 :1@N2_:2@C4 21210 0.861 4.83 0.885 64 :1@C8_:2@N4 21200 0.861 4.64 0.919 65 :1@O6_:2@N4 21023 0.854 4.4 0.9 66 :1@C8_:2@N1 20706 0.841 5.86 0.747 67 :1@N2_:2@N4 19176 0.779 5.23 0.948 68 :1@N9_:2@O2 15223 0.618 6.07 0.725 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 24626, 'v_base2' size 24626, output size 24626 TIME: Analyses took 0.0018 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 24626 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 24626 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 24626 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 24626 COM "COM" (double, distance), size is 24626 v_base2 "v_base2" (vector, vector), size is 24626 v_base1 "v_base1" (vector, vector), size is 24626 normalangle "normalangle" (double), size is 24626 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.2084 s ( 99.06%) TIME: Action Post : 0.0001 s ( 0.06%) TIME: Analysis : 0.0018 s ( 0.85%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.2104 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: 0.2800 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.