CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/26/16 12:02:55 | Available memory: 1.736 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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 45143 of 45143) Coordinate processing will occur on 45143 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.c0 (1-45143, 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 85 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@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@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@N4' 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@N4' 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@N4' 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@C6' Atom ':2@N3' to ':1@C5' Atom ':2@N3' to ':1@C4' Atom ':2@N3' to ':1@N4' 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@N4' 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 45143 frames and processed 45143 frames. TIME: Avg. throughput= 78915.6721 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 79.8777 85 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 44971 0.996 4.57 0.521 2 :2@N9_:1@N1 44881 0.994 4.87 0.629 3 :2@C4_:1@N1 44858 0.994 4.69 0.482 4 :2@C6_:1@N1 44621 0.988 4.9 0.721 5 :2@C5_:1@C6 44594 0.988 4.39 0.629 6 :2@N7_:1@N1 44589 0.988 4.66 0.622 7 :2@C4_:1@C2 44523 0.986 4.63 0.626 8 :2@C8_:1@N1 44465 0.985 4.79 0.743 9 :2@C6_:1@C6 44442 0.984 4.51 0.685 10 :2@C4_:1@C6 44429 0.984 4.79 0.651 11 :2@C5_:1@C2 44363 0.983 4.64 0.64 12 :2@N3_:1@N1 44312 0.982 5.1 0.604 13 :2@N3_:1@C2 44230 0.98 4.84 0.628 14 :2@O6_:1@C6 44098 0.977 4.71 0.752 15 :2@C6_:1@C5 44079 0.976 4.09 0.721 16 :2@N7_:1@C6 44052 0.976 4.43 0.775 17 :2@N1_:1@C4 44014 0.975 4.24 0.727 18 :2@N9_:1@C6 43998 0.975 5.11 0.763 19 :2@N9_:1@C2 43970 0.974 4.91 0.821 20 :2@C6_:1@C4 43959 0.974 4.11 0.688 21 :2@C5_:1@C5 43893 0.972 4.27 0.797 22 :2@C6_:1@C2 43891 0.972 4.84 0.828 23 :2@C4_:1@O2 43862 0.972 4.96 0.732 24 :2@N1_:1@N3 43836 0.971 4.5 0.824 25 :2@C2_:1@C2 43826 0.971 4.96 0.789 26 :2@N1_:1@C5 43825 0.971 4.45 0.799 27 :2@O6_:1@C5 43817 0.971 4.12 0.741 28 :2@N1_:1@C6 43793 0.97 4.94 0.846 29 :2@C6_:1@N3 43774 0.97 4.48 0.764 30 :2@C4_:1@N3 43748 0.969 4.67 0.828 31 :2@C2_:1@N3 43740 0.969 4.63 0.761 32 :2@C5_:1@N3 43705 0.968 4.56 0.717 33 :2@C8_:1@C6 43631 0.967 4.83 0.861 34 :2@C5_:1@C4 43604 0.966 4.38 0.794 35 :2@N3_:1@N3 43588 0.966 4.75 0.808 36 :2@O6_:1@C4 43563 0.965 4.23 0.782 37 :2@N7_:1@C2 43520 0.964 4.92 0.7 38 :2@C4_:1@C5 43461 0.963 4.81 0.865 39 :2@N1_:1@C2 43458 0.963 4.94 0.923 40 :2@N1_:1@N1 43436 0.962 5.18 0.852 41 :2@C2_:1@C4 43420 0.962 4.6 0.779 42 :2@C2_:1@N1 43373 0.961 5.27 0.796 43 :2@N3_:1@C6 43357 0.96 5.24 0.728 44 :2@O6_:1@N1 43354 0.96 5.28 0.798 45 :2@N1_:1@N4 43294 0.959 4.23 0.9 46 :2@N3_:1@O2 43289 0.959 5.04 0.814 47 :2@C4_:1@C4 43275 0.959 4.74 0.938 48 :2@N9_:1@O2 43235 0.958 5.09 0.804 49 :2@C6_:1@N4 43149 0.956 4.25 0.801 50 :2@N7_:1@C5 43068 0.954 4.53 0.875 51 :2@C5_:1@O2 43042 0.953 5.16 0.787 52 :2@C8_:1@C2 43023 0.953 5.02 0.817 53 :2@O6_:1@N4 42878 0.95 4.21 0.808 54 :2@C2_:1@C5 42747 0.947 4.9 0.814 55 :2@C2_:1@C6 42740 0.947 5.23 0.849 56 :2@O6_:1@N3 42731 0.947 4.79 0.949 57 :2@N3_:1@C4 42597 0.944 4.87 0.884 58 :2@N7_:1@N3 42168 0.934 4.99 0.803 59 :2@N7_:1@C4 42165 0.934 4.81 0.848 60 :2@C5_:1@N4 42110 0.933 4.78 0.912 61 :2@N2_:1@N3 42080 0.932 5.04 0.833 62 :2@N3_:1@C5 42067 0.932 5.12 0.809 63 :2@O6_:1@C2 41771 0.925 5.24 0.951 64 :2@N7_:1@O2 41760 0.925 5.43 0.765 65 :2@C2_:1@N4 41757 0.925 4.64 1.03 66 :2@N2_:1@C4 41552 0.92 5.07 0.798 67 :2@C8_:1@O2 41547 0.92 5.33 0.784 68 :2@C8_:1@C5 41424 0.918 5.1 0.942 69 :2@C2_:1@O2 41217 0.913 5.2 1.03 70 :2@N9_:1@N3 41015 0.909 5.1 0.976 71 :2@N2_:1@C2 40783 0.903 5.43 0.869 72 :2@N9_:1@C5 40725 0.902 5.28 0.92 73 :2@C6_:1@O2 40122 0.889 5.36 1 74 :2@C8_:1@N3 39968 0.885 5.22 0.903 75 :2@N7_:1@N4 39209 0.869 5.29 0.9 76 :2@C8_:1@C4 39055 0.865 5.24 0.925 77 :2@N2_:1@N4 39049 0.865 4.86 1 78 :2@C4_:1@N4 38892 0.862 5.06 1 79 :2@N2_:1@C5 38825 0.86 5.43 0.856 80 :2@N1_:1@O2 38674 0.857 5.3 1.12 81 :2@N3_:1@N4 38325 0.849 5.01 1.05 82 :2@N2_:1@O2 35161 0.779 5.42 1.1 83 :2@N2_:1@N1 34949 0.774 5.68 0.825 84 :2@N2_:1@C6 34620 0.767 5.68 0.943 85 :2@O6_:1@O2 30937 0.685 5.55 1.04 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 45143, 'v_base2' size 45143, output size 45143 TIME: Analyses took 0.0062 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 45143 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 45143 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 45143 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 45143 COM "COM" (double, distance), size is 45143 v_base2 "v_base2" (vector, vector), size is 45143 v_base1 "v_base1" (vector, vector), size is 45143 normalangle "normalangle" (double), size is 45143 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 0.5720 s ( 98.87%) TIME: Action Post : 0.0003 s ( 0.04%) TIME: Analysis : 0.0062 s ( 1.07%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.5786 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: 0.7790 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.