CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 15:01:32 | Available memory: 1.470 GB INPUT: Reading input from 'pt-criteria.in' [parm ../../../tip3p/ff14sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff14sb/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 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C6,C5,C4,O4,N3,C2,O2,C7' Mask2=':2@N1,C6,C5,C4,O4,N3,C2,O2,C7', 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 :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73] DISTANCE: :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73, center of mass. [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7] [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 77942 of 77942) Coordinate processing will occur on 77942 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*](37) Reference mask: [:1,2&!@H*](37) 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 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 :2@N1,C6,C5,C4,O4,N3,C2,O2,C7 mindist] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. 9 potential contact sites for ':1@N1,C6,C5,C4,O4,N3,C2,O2,C7' 9 potential contact sites for ':2@N1,C6,C5,C4,O4,N3,C2,O2,C7' Imaging enabled. 4: [distance COM :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73] :1@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,O4,N3,H3,C2,O2,C7,H71,H72,H73 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C6,C5,C4,O4,N3,C2,O2,C7 corrplane] Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2,C7 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2,C7] corresponds to 8 atoms. ----- ctraj.c0 (1-77942, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Mask [:2@N1,C6,C5,C4,O4,N3,C2,O2,C7] corresponds to 9 atoms. Setup 81 native contacts: Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C7' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@O4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@O2' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@C5' Atom ':1@C6' to ':2@C7' Atom ':1@C6' to ':2@C4' Atom ':1@C6' to ':2@O4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C7' Atom ':1@C5' to ':2@C4' Atom ':1@C5' to ':2@O4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@O2' Atom ':1@C7' to ':2@N1' Atom ':1@C7' to ':2@C6' Atom ':1@C7' to ':2@C5' Atom ':1@C7' to ':2@C7' Atom ':1@C7' to ':2@C4' Atom ':1@C7' to ':2@O4' Atom ':1@C7' to ':2@N3' Atom ':1@C7' to ':2@C2' Atom ':1@C7' to ':2@O2' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C7' Atom ':1@C4' to ':2@C4' Atom ':1@C4' to ':2@O4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' Atom ':1@O4' to ':2@N1' Atom ':1@O4' to ':2@C6' Atom ':1@O4' to ':2@C5' Atom ':1@O4' to ':2@C7' Atom ':1@O4' to ':2@C4' Atom ':1@O4' to ':2@O4' Atom ':1@O4' to ':2@N3' Atom ':1@O4' to ':2@C2' Atom ':1@O4' to ':2@O2' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C7' Atom ':1@N3' to ':2@C4' Atom ':1@N3' to ':2@O4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@O2' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C7' Atom ':1@C2' to ':2@C4' Atom ':1@C2' to ':2@O4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@O2' Atom ':1@O2' to ':2@N1' Atom ':1@O2' to ':2@C6' Atom ':1@O2' to ':2@C5' Atom ':1@O2' to ':2@C7' Atom ':1@O2' to ':2@C4' Atom ':1@O2' to ':2@O4' Atom ':1@O2' to ':2@N3' Atom ':1@O2' to ':2@C2' Atom ':1@O2' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 77942 frames and processed 77942 frames. TIME: Avg. throughput= 68838.4581 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 78.554 81 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C6 77614 0.996 4.06 0.477 2 :1@N1_:2@C5 77546 0.995 4.23 0.455 3 :1@N1_:2@N1 77477 0.994 4.35 0.423 4 :1@C2_:2@C6 77374 0.993 4.39 0.489 5 :1@C2_:2@C5 77348 0.992 4.2 0.543 6 :1@N1_:2@C4 77272 0.991 4.7 0.459 7 :1@N1_:2@C2 77246 0.991 4.81 0.507 8 :1@C6_:2@N1 77239 0.991 3.98 0.549 9 :1@C2_:2@N1 77234 0.991 4.83 0.541 10 :1@C2_:2@C4 77193 0.99 4.51 0.59 11 :1@C6_:2@C6 77186 0.99 4.01 0.547 12 :1@N1_:2@N3 77150 0.99 4.92 0.537 13 :1@C6_:2@C5 77127 0.99 4.27 0.499 14 :1@C6_:2@C2 77093 0.989 4.23 0.525 15 :1@C6_:2@C4 77035 0.988 4.52 0.447 16 :1@C6_:2@N3 77032 0.988 4.45 0.482 17 :1@O2_:2@C6 76999 0.988 4.91 0.513 18 :1@N3_:2@C4 76989 0.988 4.11 0.597 19 :1@N1_:2@C7 76976 0.988 4.59 0.541 20 :1@O2_:2@C5 76959 0.987 4.63 0.636 21 :1@N3_:2@C5 76939 0.987 4.22 0.571 22 :1@N3_:2@N3 76890 0.987 4.44 0.673 23 :1@C2_:2@N3 76877 0.986 4.91 0.665 24 :1@C5_:2@N3 76876 0.986 3.97 0.488 25 :1@C4_:2@N3 76863 0.986 3.97 0.554 26 :1@C5_:2@C2 76832 0.986 3.99 0.555 27 :1@C2_:2@C2 76814 0.986 5.1 0.675 28 :1@N1_:2@O4 76813 0.986 5.33 0.515 29 :1@C4_:2@C4 76811 0.985 3.94 0.511 30 :1@N3_:2@C6 76809 0.985 4.65 0.514 31 :1@C5_:2@C4 76784 0.985 4.15 0.478 32 :1@N3_:2@O4 76750 0.985 4.27 0.707 33 :1@C4_:2@C2 76726 0.984 4.38 0.563 34 :1@N3_:2@N1 76720 0.984 4.95 0.56 35 :1@C2_:2@C7 76701 0.984 4.34 0.72 36 :1@N3_:2@C2 76696 0.984 4.87 0.691 37 :1@C4_:2@O4 76688 0.984 4.14 0.581 38 :1@C6_:2@O4 76688 0.984 5.2 0.516 39 :1@C2_:2@O4 76674 0.984 4.88 0.684 40 :1@C5_:2@N1 76616 0.983 4.15 0.561 41 :1@C5_:2@C5 76614 0.983 4.31 0.548 42 :1@C4_:2@C5 76580 0.983 4.32 0.556 43 :1@O4_:2@N3 76569 0.982 4.14 0.607 44 :1@C5_:2@O4 76560 0.982 4.65 0.559 45 :1@C6_:2@O2 76547 0.982 4.75 0.617 46 :1@C5_:2@C6 76480 0.981 4.32 0.559 47 :1@C6_:2@C7 76454 0.981 4.95 0.613 48 :1@O4_:2@C4 76450 0.981 4.18 0.579 49 :1@O2_:2@C4 76441 0.981 5.08 0.71 50 :1@O2_:2@N1 76399 0.98 5.52 0.677 51 :1@C5_:2@O2 76393 0.98 4.4 0.667 52 :1@C4_:2@N1 76377 0.98 4.7 0.499 53 :1@O4_:2@O4 76359 0.98 4.11 0.653 54 :1@C4_:2@C6 76353 0.98 4.68 0.534 55 :1@C7_:2@N3 76327 0.979 4.16 0.591 56 :1@N1_:2@O2 76285 0.979 5.5 0.608 57 :1@C4_:2@O2 76225 0.978 4.89 0.684 58 :1@C7_:2@C4 76119 0.977 4.66 0.609 59 :1@O4_:2@C2 76085 0.976 4.75 0.607 60 :1@N3_:2@C7 76040 0.976 4.53 0.743 61 :1@C7_:2@C2 75798 0.972 4.03 0.724 62 :1@O4_:2@C5 75704 0.971 4.87 0.601 63 :1@C4_:2@C7 75394 0.967 4.94 0.666 64 :1@C5_:2@C7 75331 0.967 5.11 0.662 65 :1@C7_:2@C5 75300 0.966 5.02 0.64 66 :1@C7_:2@O4 75234 0.965 5.13 0.746 67 :1@C7_:2@C6 75194 0.965 4.94 0.609 68 :1@C7_:2@N1 75172 0.964 4.44 0.689 69 :1@O4_:2@N1 75135 0.964 5.33 0.514 70 :1@O2_:2@C7 74971 0.962 4.39 0.824 71 :1@O4_:2@O2 74906 0.961 5.12 0.725 72 :1@O4_:2@C6 74848 0.96 5.38 0.541 73 :1@C7_:2@O2 74355 0.954 4.02 0.852 74 :1@N3_:2@O2 73258 0.94 5.48 0.821 75 :1@O2_:2@O4 73112 0.938 5.28 0.781 76 :1@O2_:2@N3 72820 0.934 5.59 0.719 77 :1@O4_:2@C7 72203 0.926 5.45 0.677 78 :1@C2_:2@O2 70656 0.907 5.75 0.781 79 :1@O2_:2@C2 70248 0.901 5.78 0.774 80 :1@C7_:2@C7 66279 0.85 5.83 0.782 81 :1@O2_:2@O2 39426 0.506 5.96 0.969 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 77942, 'v_base2' size 77942, output size 77942 TIME: Analyses took 0.0058 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 77942 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 77942 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 77942 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 77942 COM "COM" (double, distance), size is 77942 v_base1 "v_base1" (vector, vector), size is 77942 v_base2 "v_base2" (vector, vector), size is 77942 normalangle "normalangle" (double), size is 77942 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0001 s ( 0.00%) TIME: Trajectory Process : 1.1322 s ( 99.47%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0058 s ( 0.51%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.1383 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: 1.4978 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.