CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:49:44 | Available memory: 3.880 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 40201 of 40201) Coordinate processing will occur on 40201 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 (1-40201, 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 40201 frames and processed 40201 frames. TIME: Avg. throughput= 58213.3016 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 80.4077 85 # Contact Nframes Frac. Avg Stdev 1 :2@N7_:1@N1 40066 0.997 4.52 0.522 2 :2@C8_:1@N1 40062 0.997 4.66 0.665 3 :2@N9_:1@N1 39991 0.995 4.8 0.589 4 :2@N7_:1@C2 39955 0.994 4.87 0.658 5 :2@C5_:1@N1 39949 0.994 4.51 0.484 6 :2@C5_:1@C2 39940 0.994 4.58 0.583 7 :2@C8_:1@C2 39807 0.99 4.99 0.783 8 :2@N7_:1@C6 39779 0.99 4.32 0.721 9 :2@N9_:1@C2 39770 0.989 4.87 0.778 10 :2@C4_:1@C2 39753 0.989 4.59 0.576 11 :2@C4_:1@N1 39749 0.989 4.68 0.46 12 :2@C5_:1@N3 39705 0.988 4.53 0.642 13 :2@C8_:1@C6 39639 0.986 4.73 0.826 14 :2@C5_:1@C6 39593 0.985 4.34 0.592 15 :2@C4_:1@O2 39548 0.984 4.92 0.707 16 :2@N7_:1@N3 39527 0.983 5.05 0.75 17 :2@C6_:1@N1 39507 0.983 4.88 0.733 18 :2@C5_:1@C4 39474 0.982 4.35 0.721 19 :2@C6_:1@N3 39469 0.982 4.42 0.723 20 :2@N9_:1@O2 39460 0.982 5.08 0.772 21 :2@C6_:1@C4 39436 0.981 4.05 0.6 22 :2@O6_:1@C4 39408 0.98 4.19 0.727 23 :2@C6_:1@C2 39360 0.979 4.79 0.829 24 :2@N7_:1@C4 39357 0.979 4.87 0.809 25 :2@C6_:1@C6 39343 0.979 4.53 0.666 26 :2@C5_:1@C5 39316 0.978 4.24 0.754 27 :2@C4_:1@N3 39302 0.978 4.62 0.792 28 :2@N7_:1@C5 39277 0.977 4.48 0.845 29 :2@O6_:1@C5 39274 0.977 4.11 0.718 30 :2@N9_:1@C6 39259 0.977 5.05 0.751 31 :2@O6_:1@C6 39255 0.976 4.71 0.755 32 :2@C4_:1@C6 39253 0.976 4.79 0.631 33 :2@C6_:1@C5 39230 0.976 4.08 0.673 34 :2@C5_:1@O2 39229 0.976 5.11 0.781 35 :2@O6_:1@N4 39200 0.975 4.2 0.759 36 :2@C6_:1@N4 39147 0.974 4.21 0.749 37 :2@N3_:1@N1 39091 0.972 5.18 0.567 38 :2@N3_:1@C2 39086 0.972 4.82 0.626 39 :2@N1_:1@N3 39065 0.972 4.41 0.797 40 :2@N1_:1@C4 38990 0.97 4.17 0.694 41 :2@N7_:1@O2 38853 0.966 5.4 0.784 42 :2@O6_:1@N3 38847 0.966 4.73 0.945 43 :2@C4_:1@C4 38780 0.965 4.69 0.919 44 :2@C5_:1@N4 38772 0.964 4.8 0.889 45 :2@C8_:1@O2 38761 0.964 5.33 0.771 46 :2@C2_:1@N3 38673 0.962 4.54 0.735 47 :2@C2_:1@C2 38657 0.962 4.95 0.796 48 :2@C4_:1@C5 38632 0.961 4.79 0.855 49 :2@N1_:1@C5 38597 0.96 4.49 0.77 50 :2@N3_:1@O2 38550 0.959 5 0.823 51 :2@N1_:1@N4 38549 0.959 4.09 0.839 52 :2@N1_:1@C2 38542 0.959 4.92 0.935 53 :2@O6_:1@N1 38533 0.959 5.24 0.816 54 :2@N1_:1@C6 38526 0.958 5.06 0.785 55 :2@N3_:1@N3 38518 0.958 4.66 0.799 56 :2@C8_:1@C5 38265 0.952 5.08 0.938 57 :2@N1_:1@N1 38243 0.951 5.26 0.856 58 :2@C2_:1@C4 38154 0.949 4.53 0.779 59 :2@C2_:1@N1 38120 0.948 5.39 0.759 60 :2@N3_:1@C6 38043 0.946 5.35 0.672 61 :2@N9_:1@N3 37915 0.943 5.13 0.971 62 :2@C8_:1@N3 37757 0.939 5.31 0.868 63 :2@O6_:1@C2 37729 0.939 5.18 0.973 64 :2@N3_:1@C4 37445 0.931 4.79 0.894 65 :2@C2_:1@C5 37431 0.931 4.97 0.804 66 :2@C2_:1@C6 37387 0.93 5.39 0.746 67 :2@N2_:1@N3 37192 0.925 4.98 0.792 68 :2@N9_:1@C5 36922 0.918 5.26 0.922 69 :2@C2_:1@N4 36858 0.917 4.48 0.994 70 :2@N3_:1@C5 36833 0.916 5.14 0.819 71 :2@N7_:1@N4 36737 0.914 5.42 0.824 72 :2@C8_:1@C4 36683 0.912 5.32 0.912 73 :2@C2_:1@O2 36599 0.91 5.17 1.03 74 :2@C6_:1@O2 36449 0.907 5.31 1.02 75 :2@N2_:1@C4 36409 0.906 5.02 0.786 76 :2@N2_:1@C2 35644 0.887 5.46 0.863 77 :2@C4_:1@N4 35436 0.881 5.03 1.02 78 :2@N2_:1@N4 34753 0.864 4.72 0.954 79 :2@N1_:1@O2 34593 0.861 5.25 1.13 80 :2@N3_:1@N4 33956 0.845 4.87 1.03 81 :2@N2_:1@C5 33474 0.833 5.55 0.81 82 :2@N2_:1@O2 30878 0.768 5.38 1.09 83 :2@N2_:1@N1 29531 0.735 5.87 0.739 84 :2@N2_:1@C6 29197 0.726 5.93 0.766 85 :2@O6_:1@O2 28424 0.707 5.48 1.06 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 40201, 'v_base2' size 40201, output size 40201 TIME: Analyses took 0.0055 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 40201 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 40201 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 40201 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 40201 COM "COM" (double, distance), size is 40201 v_base2 "v_base2" (vector, vector), size is 40201 v_base1 "v_base1" (vector, vector), size is 40201 normalangle "normalangle" (double), size is 40201 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0000 s ( 0.01%) TIME: Trajectory Process : 0.6906 s ( 99.16%) TIME: Action Post : 0.0003 s ( 0.04%) TIME: Analysis : 0.0055 s ( 0.79%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.6964 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: 1.5036 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.