CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:18:00 | Available memory: 1.228 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,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.c0' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 307653 of 307653) Coordinate processing will occur on 307653 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.c0 (1-307653, 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 79 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@N4' 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@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@N4' 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@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 307653 frames and processed 307653 frames. TIME: Avg. throughput= 103854.2672 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 71.9618 79 # Contact Nframes Frac. Avg Stdev 1 :2@N7_:1@N1 303715 0.987 4.66 0.691 2 :2@C5_:1@N1 303538 0.987 4.64 0.578 3 :2@N9_:1@N1 302386 0.983 5.07 0.655 4 :2@C8_:1@N1 302286 0.983 4.87 0.795 5 :2@C4_:1@N1 300534 0.977 4.88 0.526 6 :2@C5_:1@C2 300426 0.977 4.66 0.717 7 :2@N7_:1@C6 299395 0.973 4.55 0.863 8 :2@C5_:1@C6 298794 0.971 4.58 0.676 9 :2@C4_:1@C2 298729 0.971 4.85 0.669 10 :2@C6_:1@N1 297419 0.967 4.87 0.803 11 :2@C6_:1@C6 295538 0.961 4.68 0.766 12 :2@N7_:1@C2 295405 0.96 4.84 0.827 13 :2@C6_:1@C2 295015 0.959 4.73 0.891 14 :2@N9_:1@C2 294786 0.958 5.14 0.863 15 :2@C6_:1@N3 294725 0.958 4.48 0.818 16 :2@C6_:1@C4 294630 0.958 4.31 0.728 17 :2@C5_:1@N3 294374 0.957 4.66 0.778 18 :2@C4_:1@C6 294372 0.957 5.04 0.687 19 :2@N6_:1@C6 294344 0.957 4.79 0.833 20 :2@N6_:1@C5 294056 0.956 4.29 0.809 21 :2@N6_:1@C4 293961 0.955 4.23 0.843 22 :2@C5_:1@C5 293937 0.955 4.56 0.846 23 :2@C6_:1@C5 293529 0.954 4.38 0.772 24 :2@C5_:1@C4 293166 0.953 4.62 0.847 25 :2@C8_:1@C6 293005 0.952 4.95 0.928 26 :2@C4_:1@O2 291999 0.949 5.04 0.787 27 :2@N9_:1@C6 291561 0.948 5.31 0.802 28 :2@N3_:1@N1 291435 0.947 5.31 0.666 29 :2@N3_:1@C2 290683 0.945 5.12 0.688 30 :2@C4_:1@N3 290363 0.944 4.98 0.892 31 :2@N1_:1@N3 290227 0.943 4.65 0.86 32 :2@C8_:1@C2 289999 0.943 5.07 0.889 33 :2@N1_:1@C4 289834 0.942 4.56 0.801 34 :2@N7_:1@C5 289784 0.942 4.67 0.977 35 :2@N6_:1@N4 288502 0.938 4.25 0.865 36 :2@N6_:1@N1 287935 0.936 5.13 0.883 37 :2@C5_:1@O2 287651 0.935 5 0.891 38 :2@N6_:1@N3 287517 0.935 4.53 1.04 39 :2@C6_:1@N4 287235 0.934 4.51 0.875 40 :2@N7_:1@N3 286744 0.932 4.97 0.902 41 :2@C2_:1@C2 286407 0.931 5.11 0.85 42 :2@N9_:1@O2 286375 0.931 5.24 0.863 43 :2@N7_:1@C4 285534 0.928 4.9 0.932 44 :2@N1_:1@C2 285227 0.927 4.94 0.973 45 :2@C4_:1@C5 284734 0.926 5.14 0.915 46 :2@C2_:1@N3 284482 0.925 4.94 0.813 47 :2@C4_:1@C4 284040 0.923 5.1 1.01 48 :2@N1_:1@C5 283721 0.922 4.76 0.897 49 :2@N1_:1@C6 282403 0.918 5.11 0.971 50 :2@N1_:1@N4 282397 0.918 4.61 0.969 51 :2@N1_:1@N1 281866 0.916 5.2 0.965 52 :2@N3_:1@O2 281613 0.915 5.19 0.852 53 :2@N7_:1@O2 280813 0.913 5.2 0.957 54 :2@N3_:1@N3 280621 0.912 5.12 0.883 55 :2@N6_:1@C2 280479 0.912 4.93 1.05 56 :2@C2_:1@N1 280231 0.911 5.37 0.894 57 :2@C2_:1@C4 278363 0.905 4.99 0.878 58 :2@C5_:1@N4 278089 0.904 5.02 0.986 59 :2@C8_:1@O2 274272 0.891 5.26 0.886 60 :2@N3_:1@C6 273812 0.89 5.46 0.742 61 :2@C8_:1@C5 268795 0.874 5.2 1.01 62 :2@C6_:1@O2 268722 0.873 5.04 1.06 63 :2@N3_:1@C4 266583 0.867 5.26 0.983 64 :2@C2_:1@C5 264880 0.861 5.17 0.871 65 :2@C2_:1@C6 264298 0.859 5.36 0.901 66 :2@C2_:1@O2 263497 0.856 5.17 1.03 67 :2@N9_:1@N3 261931 0.851 5.34 1.04 68 :2@C8_:1@N3 261645 0.85 5.29 0.937 69 :2@N3_:1@C5 259385 0.843 5.42 0.857 70 :2@N9_:1@C5 258309 0.84 5.5 0.993 71 :2@N7_:1@N4 255652 0.831 5.34 0.912 72 :2@C2_:1@N4 254463 0.827 5.02 1.1 73 :2@N1_:1@O2 251766 0.818 5.07 1.12 74 :2@C8_:1@C4 251144 0.816 5.34 0.971 75 :2@N9_:1@C4 235200 0.764 5.42 1.06 76 :2@C4_:1@N4 233754 0.76 5.32 1.13 77 :2@N6_:1@O2 224004 0.728 5.08 1.07 78 :2@N3_:1@N4 211346 0.687 5.24 1.16 79 :2@C8_:1@N4 184884 0.601 5.62 0.811 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 307653, 'v_base2' size 307653, output size 307653 TIME: Analyses took 0.0218 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 307653 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 307653 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 307653 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 307653 COM "COM" (double, distance), size is 307653 v_base2 "v_base2" (vector, vector), size is 307653 v_base1 "v_base1" (vector, vector), size is 307653 normalangle "normalangle" (double), size is 307653 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0022 s ( 0.07%) TIME: Trajectory Process : 2.9624 s ( 99.19%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0218 s ( 0.73%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.9866 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: 3.8043 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.