CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 17:04:03 | Available memory: 3.911 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.c0] Reading '../ctraj.c0' 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,O4,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,O4,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,O4,N3,H3,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,O4,N3,H3,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,O4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 67220 of 67220) Coordinate processing will occur on 67220 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,O4,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,O4,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,O4,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,O4,N3,H3,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,O4,N3,H3,C2,O2 (11 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,O4,N3,C2,O2 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c0 (1-67220, 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,O4,N3,C2,O2] corresponds to 8 atoms. Setup 75 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@N9' to ':1@C5' Atom ':2@N9' to ':1@C4' Atom ':2@N9' to ':1@N3' 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@C5' Atom ':2@C8' to ':1@C4' Atom ':2@C8' to ':1@O4' Atom ':2@C8' to ':1@N3' 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@O4' 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@O4' 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@O4' 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@O4' 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@O4' 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@C4' Atom ':2@C2' to ':1@N3' Atom ':2@C2' to ':1@C2' Atom ':2@C2' to ':1@O2' Atom ':2@N2' to ':1@N3' Atom ':2@N2' to ':1@C2' Atom ':2@N2' to ':1@O2' Atom ':2@N3' to ':1@N1' 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@O4' 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 67220 frames and processed 67220 frames. TIME: Avg. throughput= 102753.8082 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 69.7094 75 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 66722 0.993 4.56 0.532 2 :2@C4_:1@N1 66543 0.99 4.82 0.477 3 :2@N9_:1@N1 66511 0.989 5.27 0.565 4 :2@C6_:1@N1 66307 0.986 4.58 0.637 5 :2@N7_:1@N1 66077 0.983 4.81 0.735 6 :2@C4_:1@C2 66057 0.983 4.69 0.589 7 :2@C5_:1@C6 65971 0.981 4.85 0.72 8 :2@C6_:1@C6 65969 0.981 4.74 0.757 9 :2@C5_:1@C2 65815 0.979 4.34 0.659 10 :2@N3_:1@N1 65789 0.979 5.1 0.659 11 :2@C4_:1@C6 65776 0.979 5.29 0.701 12 :2@O6_:1@N1 65626 0.976 4.86 0.728 13 :2@N1_:1@N1 65592 0.976 4.81 0.798 14 :2@C8_:1@N1 65549 0.975 5.18 0.74 15 :2@C6_:1@C2 65521 0.975 4.18 0.781 16 :2@N3_:1@C2 65391 0.973 4.89 0.603 17 :2@O6_:1@C6 65304 0.971 4.82 0.802 18 :2@C6_:1@C5 65295 0.971 4.59 0.833 19 :2@N1_:1@C2 65242 0.971 4.36 0.828 20 :2@N9_:1@C2 65211 0.97 5.26 0.694 21 :2@C6_:1@C4 65097 0.968 4.29 0.691 22 :2@C2_:1@C2 65071 0.968 4.69 0.731 23 :2@C6_:1@N3 65066 0.968 4.03 0.723 24 :2@C2_:1@N1 65054 0.968 5.02 0.829 25 :2@C4_:1@O2 65049 0.968 4.62 0.767 26 :2@N1_:1@N3 65000 0.967 4.23 0.75 27 :2@C5_:1@N3 64928 0.966 4.51 0.703 28 :2@N1_:1@C4 64894 0.965 4.54 0.822 29 :2@N7_:1@C2 64883 0.965 4.73 0.784 30 :2@O6_:1@C5 64782 0.964 4.41 0.857 31 :2@O6_:1@C4 64762 0.963 4 0.772 32 :2@C4_:1@N3 64697 0.962 5.07 0.701 33 :2@O6_:1@N3 64568 0.961 3.94 0.923 34 :2@O6_:1@C2 64518 0.96 4.37 0.913 35 :2@C2_:1@N3 64493 0.959 4.81 0.723 36 :2@C5_:1@O2 64484 0.959 4.43 0.885 37 :2@N3_:1@O2 64405 0.958 4.75 0.795 38 :2@C5_:1@C4 64269 0.956 4.87 0.75 39 :2@C5_:1@C5 64258 0.956 4.97 0.815 40 :2@N3_:1@N3 64131 0.954 5.26 0.712 41 :2@N1_:1@C6 64109 0.954 4.98 0.966 42 :2@C8_:1@C2 63981 0.952 5.2 0.774 43 :2@N9_:1@O2 63980 0.952 5.12 0.77 44 :2@O6_:1@O4 63826 0.95 4.14 0.798 45 :2@N1_:1@C5 63825 0.949 4.84 1.02 46 :2@C6_:1@O4 63804 0.949 4.64 0.761 47 :2@N1_:1@O4 63389 0.943 4.85 0.903 48 :2@C2_:1@O2 63372 0.943 4.6 0.959 49 :2@C6_:1@O2 63366 0.943 4.34 1.02 50 :2@N7_:1@N3 63085 0.938 4.93 0.869 51 :2@N7_:1@O2 62983 0.937 4.82 0.911 52 :2@C4_:1@C4 62966 0.937 5.55 0.807 53 :2@C4_:1@C5 62952 0.937 5.6 0.827 54 :2@N1_:1@O2 62670 0.932 4.4 1.05 55 :2@N9_:1@C6 62572 0.931 5.73 0.706 56 :2@N7_:1@C6 62479 0.929 4.93 0.876 57 :2@C2_:1@C4 62464 0.929 5.2 0.881 58 :2@N2_:1@C2 62231 0.926 5.21 0.836 59 :2@C8_:1@O2 62112 0.924 5.16 0.836 60 :2@N2_:1@N3 61380 0.913 5.26 0.852 61 :2@C5_:1@O4 60995 0.907 5.37 0.808 62 :2@N7_:1@C4 60606 0.902 5.18 0.87 63 :2@N9_:1@N3 59694 0.888 5.72 0.804 64 :2@N7_:1@C5 59474 0.885 5.08 0.891 65 :2@O6_:1@O2 59451 0.884 4.54 1.01 66 :2@N2_:1@O2 59309 0.882 5.01 0.994 67 :2@C8_:1@C6 58907 0.876 5.38 0.814 68 :2@C8_:1@N3 58742 0.874 5.56 0.844 69 :2@N7_:1@O4 54085 0.805 5.63 0.865 70 :2@C8_:1@C5 52687 0.784 5.68 0.832 71 :2@C8_:1@C4 50932 0.758 5.81 0.834 72 :2@N9_:1@C5 50677 0.754 6.02 0.799 73 :2@C4_:1@O4 49965 0.743 5.97 0.874 74 :2@N9_:1@C4 47194 0.702 6.03 0.829 75 :2@C8_:1@O4 30928 0.46 5.98 0.763 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 67220, 'v_base2' size 67220, output size 67220 TIME: Analyses took 0.0091 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 67220 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 67220 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 67220 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 67220 COM "COM" (double, distance), size is 67220 v_base2 "v_base2" (vector, vector), size is 67220 v_base1 "v_base1" (vector, vector), size is 67220 normalangle "normalangle" (double), size is 67220 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.01%) TIME: Trajectory Process : 0.6542 s ( 98.58%) TIME: Action Post : 0.0002 s ( 0.04%) TIME: Analysis : 0.0091 s ( 1.36%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6636 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: 0.9871 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.