CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 15:01:33 | Available memory: 1.469 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.c1] Reading '../ctraj.c1' 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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 11651 of 11651) Coordinate processing will occur on 11651 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.c1 (1-11651, 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 78 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@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@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@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 11651 frames and processed 11651 frames. TIME: Avg. throughput= 73198.9269 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 50.8259 78 # Contact Nframes Frac. Avg Stdev 1 :1@N1_:2@C5 11324 0.972 4.67 0.781 2 :1@N1_:2@C6 11275 0.968 5.13 0.742 3 :1@N1_:2@C7 11256 0.966 4.54 0.709 4 :1@C6_:2@C7 11079 0.951 4.7 0.863 5 :1@C2_:2@C7 10956 0.94 4.93 0.906 6 :1@C2_:2@C5 10955 0.94 5.04 0.84 7 :1@O2_:2@C5 10890 0.935 5.18 0.832 8 :1@C6_:2@C5 10868 0.933 5.02 0.854 9 :1@N1_:2@C4 10853 0.932 4.77 0.939 10 :1@O2_:2@C6 10626 0.912 5.59 0.781 11 :1@O2_:2@C7 10603 0.91 5.19 0.999 12 :1@C2_:2@C6 10509 0.902 5.55 0.767 13 :1@N1_:2@O4 10481 0.9 4.78 0.982 14 :1@C2_:2@C4 10435 0.896 4.92 0.944 15 :1@O2_:2@C4 10404 0.893 5.01 0.939 16 :1@N1_:2@N1 10397 0.892 5.61 0.724 17 :1@C6_:2@C6 10305 0.884 5.53 0.76 18 :1@C2_:2@O4 10193 0.875 4.78 1.03 19 :1@C5_:2@C7 10080 0.865 5.1 0.943 20 :1@O2_:2@O4 10032 0.861 4.95 1.04 21 :1@C6_:2@C4 10011 0.859 5.04 0.919 22 :1@C6_:2@O4 9803 0.841 4.91 1.02 23 :1@N1_:2@N3 9656 0.829 5.13 0.864 24 :1@O2_:2@N1 9634 0.827 5.86 0.698 25 :1@N3_:2@C7 9518 0.817 5.18 0.943 26 :1@O2_:2@N3 9394 0.806 5.18 0.965 27 :1@N3_:2@O4 9370 0.804 4.94 1.05 28 :1@N3_:2@C5 9292 0.798 5.48 0.834 29 :1@C5_:2@C5 9292 0.798 5.5 0.821 30 :1@N3_:2@C4 9212 0.791 5.29 0.904 31 :1@C2_:2@N3 9210 0.79 5.23 0.877 32 :1@N1_:2@C2 9107 0.782 5.54 0.725 33 :1@C2_:2@N1 9025 0.775 5.91 0.676 34 :1@C5_:2@O4 8984 0.771 5.08 0.968 35 :1@C4_:2@C7 8907 0.764 5.28 0.93 36 :1@C4_:2@O4 8770 0.753 5.13 0.961 37 :1@O2_:2@C2 8761 0.752 5.6 0.783 38 :1@C5_:2@C4 8732 0.749 5.4 0.822 39 :1@C6_:2@N3 8453 0.726 5.48 0.795 40 :1@C7_:2@C7 8448 0.725 5.45 0.869 41 :1@C2_:2@C2 8327 0.715 5.72 0.701 42 :1@C4_:2@C4 8184 0.702 5.53 0.799 43 :1@C6_:2@N1 8128 0.698 5.97 0.643 44 :1@C4_:2@C5 8081 0.694 5.68 0.789 45 :1@N3_:2@N3 7646 0.656 5.67 0.759 46 :1@C7_:2@O4 7431 0.638 5.51 0.915 47 :1@O4_:2@O4 7383 0.634 5.52 0.858 48 :1@C6_:2@C2 7300 0.627 5.93 0.633 49 :1@N3_:2@C6 7169 0.615 5.98 0.684 50 :1@C5_:2@C6 6989 0.6 5.97 0.657 51 :1@N1_:2@O2 6962 0.598 6.01 0.601 52 :1@C5_:2@N3 6819 0.585 5.89 0.664 53 :1@C7_:2@C5 6793 0.583 5.92 0.661 54 :1@O4_:2@C7 6766 0.581 5.62 0.821 55 :1@O2_:2@O2 6750 0.579 5.83 0.716 56 :1@C7_:2@C4 6609 0.567 5.88 0.707 57 :1@C4_:2@N3 6342 0.544 6.03 0.617 58 :1@C2_:2@O2 6096 0.523 6.09 0.609 59 :1@O4_:2@C4 5950 0.511 5.96 0.662 60 :1@N3_:2@C2 5475 0.47 6.2 0.564 61 :1@C4_:2@C6 5245 0.45 6.13 0.597 62 :1@O4_:2@C5 5170 0.444 6.03 0.623 63 :1@N3_:2@N1 4676 0.401 6.28 0.547 64 :1@C5_:2@C2 4292 0.368 6.36 0.518 65 :1@C6_:2@O2 4198 0.36 6.29 0.586 66 :1@C5_:2@N1 4059 0.348 6.33 0.5 67 :1@C7_:2@C6 3821 0.328 6.27 0.524 68 :1@C7_:2@N3 3671 0.315 6.2 0.637 69 :1@O4_:2@N3 3241 0.278 6.36 0.535 70 :1@C4_:2@C2 3034 0.26 6.46 0.493 71 :1@N3_:2@O2 2665 0.229 6.42 0.559 72 :1@C4_:2@N1 2551 0.219 6.44 0.466 73 :1@O4_:2@C6 2205 0.189 6.4 0.463 74 :1@C5_:2@O2 1338 0.115 6.46 0.597 75 :1@C7_:2@C2 1218 0.105 6.44 0.553 76 :1@C7_:2@N1 1199 0.103 6.54 0.484 77 :1@C4_:2@O2 751 0.0645 6.44 0.627 78 :1@O4_:2@C2 539 0.0463 6.43 0.586 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 11651, 'v_base2' size 11651, output size 11651 TIME: Analyses took 0.0014 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 11651 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 11651 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 11651 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 11651 COM "COM" (double, distance), size is 11651 v_base1 "v_base1" (vector, vector), size is 11651 v_base2 "v_base2" (vector, vector), size is 11651 normalangle "normalangle" (double), size is 11651 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.02%) TIME: Trajectory Process : 0.1592 s ( 98.92%) TIME: Action Post : 0.0002 s ( 0.14%) TIME: Analysis : 0.0014 s ( 0.89%) TIME: Data File Write : 0.0000 s ( 0.01%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.1609 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: 0.2355 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.