CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:43:49 | Available memory: 3.960 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 61664 of 61664) Coordinate processing will occur on 61664 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 (1-61664, 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 61664 frames and processed 61664 frames. TIME: Avg. throughput= 57204.2959 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 79.2612 85 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 61175 0.992 4.63 0.539 2 :2@C4_:1@N1 61030 0.99 4.72 0.484 3 :2@N9_:1@N1 61001 0.989 5.05 0.683 4 :2@C4_:1@C2 60782 0.986 4.66 0.62 5 :2@C6_:1@N1 60753 0.985 4.81 0.686 6 :2@C5_:1@C2 60651 0.984 4.6 0.636 7 :2@N7_:1@N1 60511 0.981 4.88 0.748 8 :2@N3_:1@N1 60420 0.98 4.96 0.619 9 :2@N3_:1@C2 60337 0.978 4.8 0.617 10 :2@C6_:1@C6 60286 0.978 4.58 0.73 11 :2@C5_:1@C6 60223 0.977 4.6 0.778 12 :2@C4_:1@O2 60189 0.976 4.88 0.75 13 :2@C4_:1@C6 60182 0.976 4.92 0.694 14 :2@C6_:1@C2 60160 0.976 4.66 0.822 15 :2@C6_:1@N3 59940 0.972 4.37 0.768 16 :2@C2_:1@C2 59921 0.972 4.78 0.803 17 :2@N9_:1@C2 59909 0.972 5.06 0.822 18 :2@C8_:1@N1 59894 0.971 5.06 0.858 19 :2@C6_:1@C4 59882 0.971 4.17 0.71 20 :2@N1_:1@C4 59841 0.97 4.2 0.722 21 :2@C5_:1@N3 59828 0.97 4.6 0.732 22 :2@N1_:1@N3 59817 0.97 4.36 0.821 23 :2@C6_:1@C5 59685 0.968 4.24 0.801 24 :2@C4_:1@N3 59676 0.968 4.81 0.828 25 :2@N1_:1@C2 59646 0.967 4.7 0.939 26 :2@O6_:1@C6 59625 0.967 4.82 0.812 27 :2@N1_:1@C6 59622 0.967 4.78 0.845 28 :2@N1_:1@N1 59549 0.966 4.93 0.875 29 :2@C2_:1@N3 59505 0.965 4.6 0.734 30 :2@N1_:1@C5 59490 0.965 4.39 0.788 31 :2@O6_:1@C4 59479 0.965 4.23 0.787 32 :2@N3_:1@O2 59462 0.964 4.97 0.784 33 :2@C2_:1@N1 59459 0.964 5 0.859 34 :2@N7_:1@C2 59447 0.964 4.97 0.718 35 :2@O6_:1@N1 59431 0.964 5.21 0.753 36 :2@C5_:1@O2 59371 0.963 4.96 0.866 37 :2@N3_:1@N3 59247 0.961 4.85 0.782 38 :2@O6_:1@C5 59241 0.961 4.28 0.851 39 :2@C5_:1@C4 59196 0.96 4.58 0.849 40 :2@N3_:1@C6 59138 0.959 5.17 0.706 41 :2@C2_:1@C4 58935 0.956 4.61 0.743 42 :2@O6_:1@N3 58894 0.955 4.59 0.95 43 :2@N9_:1@O2 58835 0.954 5.12 0.807 44 :2@C5_:1@C5 58801 0.954 4.54 0.924 45 :2@N1_:1@N4 58765 0.953 4.3 0.865 46 :2@C6_:1@N4 58690 0.952 4.38 0.831 47 :2@O6_:1@N4 58511 0.949 4.25 0.843 48 :2@C2_:1@C6 58508 0.949 5.01 0.874 49 :2@C4_:1@C4 58400 0.947 4.96 0.949 50 :2@C2_:1@C5 58288 0.945 4.83 0.79 51 :2@C4_:1@C5 58246 0.945 5.02 0.896 52 :2@C8_:1@C2 58157 0.943 5.15 0.825 53 :2@O6_:1@C2 58008 0.941 5.02 0.937 54 :2@N3_:1@C4 57823 0.938 5.02 0.859 55 :2@N2_:1@N3 57516 0.933 4.98 0.815 56 :2@N9_:1@C6 57324 0.93 5.31 0.829 57 :2@N3_:1@C5 57321 0.93 5.19 0.773 58 :2@C2_:1@O2 57282 0.929 5.03 0.99 59 :2@N7_:1@N3 57261 0.929 5.07 0.817 60 :2@N7_:1@O2 56925 0.923 5.24 0.848 61 :2@C2_:1@N4 56840 0.922 4.81 0.988 62 :2@N2_:1@C4 56834 0.922 4.99 0.778 63 :2@N7_:1@C6 56699 0.919 4.72 0.971 64 :2@N2_:1@C2 56550 0.917 5.21 0.904 65 :2@C6_:1@O2 56463 0.916 5.07 1.06 66 :2@C5_:1@N4 56210 0.912 4.98 0.94 67 :2@C8_:1@O2 55943 0.907 5.26 0.793 68 :2@N7_:1@C4 55650 0.902 5.04 0.911 69 :2@N1_:1@O2 54826 0.889 5.04 1.11 70 :2@N9_:1@N3 54660 0.886 5.31 0.973 71 :2@N7_:1@C5 54379 0.882 4.79 1 72 :2@N2_:1@C5 54138 0.878 5.19 0.917 73 :2@C8_:1@C6 53918 0.874 5.06 0.961 74 :2@N2_:1@N4 53853 0.873 5 0.967 75 :2@C8_:1@N3 52734 0.855 5.37 0.895 76 :2@N3_:1@N4 51360 0.833 5.28 1.06 77 :2@N2_:1@O2 50787 0.824 5.3 1.05 78 :2@N2_:1@N1 50759 0.823 5.3 0.957 79 :2@C4_:1@N4 50746 0.823 5.3 1.02 80 :2@N9_:1@C5 50402 0.817 5.48 0.947 81 :2@N2_:1@C6 50151 0.813 5.29 1.07 82 :2@N7_:1@N4 49441 0.802 5.43 0.897 83 :2@C8_:1@C5 49320 0.8 5.27 0.985 84 :2@C8_:1@C4 48350 0.784 5.42 0.943 85 :2@O6_:1@O2 47061 0.763 5.26 1.08 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 61664, 'v_base2' size 61664, output size 61664 TIME: Analyses took 0.0084 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 61664 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 61664 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 61664 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 61664 COM "COM" (double, distance), size is 61664 v_base2 "v_base2" (vector, vector), size is 61664 v_base1 "v_base1" (vector, vector), size is 61664 normalangle "normalangle" (double), size is 61664 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 1.0780 s ( 99.19%) TIME: Action Post : 0.0003 s ( 0.02%) TIME: Analysis : 0.0084 s ( 0.78%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.0868 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: 2.2600 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.