CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/31/16 15:22:01 | Available memory: 3.002 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 48868 of 48868) Coordinate processing will occur on 48868 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 (1-48868, 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 48868 frames and processed 48868 frames. TIME: Avg. throughput= 64795.7729 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 70.9433 75 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@C2 48789 0.998 4.18 0.502 2 :2@C5_:1@N1 48774 0.998 4.48 0.473 3 :2@C5_:1@O2 48726 0.997 4.16 0.705 4 :2@C4_:1@C2 48696 0.996 4.67 0.471 5 :2@C6_:1@C2 48694 0.996 3.87 0.479 6 :2@N9_:1@N1 48685 0.996 5.37 0.452 7 :2@O6_:1@C2 48684 0.996 4 0.57 8 :2@C6_:1@O2 48678 0.996 3.95 0.688 9 :2@C4_:1@O2 48672 0.996 4.47 0.676 10 :2@C4_:1@N1 48640 0.995 4.85 0.423 11 :2@C5_:1@N3 48636 0.995 4.49 0.61 12 :2@N7_:1@C2 48635 0.995 4.65 0.743 13 :2@O6_:1@N3 48627 0.995 3.59 0.622 14 :2@O6_:1@O2 48588 0.994 4.24 0.75 15 :2@C6_:1@N3 48579 0.994 3.82 0.532 16 :2@N9_:1@C2 48536 0.993 5.38 0.547 17 :2@C6_:1@N1 48532 0.993 4.41 0.53 18 :2@N7_:1@N1 48524 0.993 4.76 0.727 19 :2@O6_:1@N1 48478 0.992 4.63 0.604 20 :2@O6_:1@C4 48395 0.99 3.88 0.687 21 :2@N1_:1@C2 48337 0.989 4.07 0.613 22 :2@C6_:1@C4 48334 0.989 4.32 0.599 23 :2@N9_:1@O2 48266 0.988 5.16 0.711 24 :2@C4_:1@N3 48250 0.987 5.21 0.539 25 :2@N1_:1@N3 48229 0.987 4.06 0.638 26 :2@N1_:1@O2 48220 0.987 4.02 0.754 27 :2@C6_:1@C6 48181 0.986 4.81 0.749 28 :2@N3_:1@C2 48170 0.986 4.89 0.555 29 :2@N1_:1@N1 48163 0.986 4.67 0.746 30 :2@N7_:1@O2 48141 0.985 4.67 0.856 31 :2@C5_:1@C6 48122 0.985 4.97 0.669 32 :2@O6_:1@O4 48103 0.984 4.1 0.731 33 :2@C8_:1@N1 48099 0.984 5.24 0.688 34 :2@C8_:1@C2 48090 0.984 5.28 0.711 35 :2@N3_:1@N1 48075 0.984 5.14 0.648 36 :2@N3_:1@O2 48037 0.983 4.6 0.732 37 :2@C2_:1@C2 48036 0.983 4.54 0.668 38 :2@N7_:1@N3 47989 0.982 4.98 0.835 39 :2@C5_:1@C4 47968 0.982 5.03 0.586 40 :2@C4_:1@C6 47945 0.981 5.49 0.602 41 :2@C6_:1@C5 47941 0.981 4.76 0.757 42 :2@C6_:1@O4 47874 0.98 4.77 0.639 43 :2@O6_:1@C6 47862 0.979 4.82 0.816 44 :2@N1_:1@C4 47834 0.979 4.61 0.805 45 :2@C2_:1@O2 47774 0.978 4.31 0.803 46 :2@O6_:1@C5 47770 0.978 4.48 0.849 47 :2@C2_:1@N3 47688 0.976 4.82 0.688 48 :2@C2_:1@N1 47644 0.975 4.98 0.823 49 :2@N3_:1@N3 47448 0.971 5.42 0.576 50 :2@C8_:1@O2 47230 0.966 5.16 0.809 51 :2@C5_:1@C5 47160 0.965 5.2 0.64 52 :2@N1_:1@O4 47034 0.962 5.04 0.796 53 :2@C4_:1@C4 46660 0.955 5.84 0.502 54 :2@N1_:1@C6 46454 0.951 5.07 0.973 55 :2@N1_:1@C5 46374 0.949 5.04 1.01 56 :2@N2_:1@C2 46372 0.949 5.1 0.825 57 :2@C5_:1@O4 45905 0.939 5.62 0.586 58 :2@N2_:1@O2 45807 0.937 4.78 0.909 59 :2@C4_:1@C5 45785 0.937 5.91 0.569 60 :2@C2_:1@C4 45589 0.933 5.42 0.813 61 :2@N7_:1@C4 45520 0.931 5.34 0.793 62 :2@N7_:1@C6 45255 0.926 5.02 0.837 63 :2@N9_:1@C6 45199 0.925 5.95 0.53 64 :2@N2_:1@N3 45167 0.924 5.3 0.84 65 :2@N9_:1@N3 44645 0.914 5.98 0.549 66 :2@C8_:1@N3 44395 0.908 5.76 0.723 67 :2@N7_:1@C5 43285 0.886 5.26 0.789 68 :2@C8_:1@C6 42094 0.861 5.52 0.694 69 :2@N7_:1@O4 40226 0.823 5.85 0.74 70 :2@C8_:1@C5 37438 0.766 5.92 0.642 71 :2@C8_:1@C4 36858 0.754 6.08 0.653 72 :2@C4_:1@O4 35234 0.721 6.36 0.434 73 :2@N9_:1@C5 34898 0.714 6.36 0.458 74 :2@N9_:1@C4 32773 0.671 6.4 0.432 75 :2@C8_:1@O4 18341 0.375 6.3 0.557 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 48868, 'v_base2' size 48868, output size 48868 TIME: Analyses took 0.0041 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 48868 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 48868 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 48868 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 48868 COM "COM" (double, distance), size is 48868 v_base2 "v_base2" (vector, vector), size is 48868 v_base1 "v_base1" (vector, vector), size is 48868 normalangle "normalangle" (double), size is 48868 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.7542 s ( 99.43%) TIME: Action Post : 0.0001 s ( 0.02%) TIME: Analysis : 0.0041 s ( 0.54%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.7585 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: 0.9858 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.