CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 14:34:07 | Available memory: 1.656 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.c2] Reading '../ctraj.c2' 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.c2' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 88741 of 88741) Coordinate processing will occur on 88741 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.c2 (1-88741, 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 59 native contacts: Atom ':2@N9' to ':1@N1' Atom ':2@N9' to ':1@C6' Atom ':2@C8' to ':1@N1' Atom ':2@C8' to ':1@C6' 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@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@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@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@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@C2' Atom ':2@C4' to ':1@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 88741 frames and processed 88741 frames. TIME: Avg. throughput= 102597.8681 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 2 1 50.2232 59 # Contact Nframes Frac. Avg Stdev 1 :2@C5_:1@N1 85972 0.969 4.67 0.708 2 :2@N7_:1@N1 85572 0.964 5.02 0.737 3 :2@C6_:1@N1 85296 0.961 4.29 0.759 4 :2@N6_:1@N1 85127 0.959 4.19 0.784 5 :2@N6_:1@C6 83624 0.942 4.33 0.877 6 :2@C4_:1@N1 83528 0.941 5.23 0.623 7 :2@C6_:1@C6 83474 0.941 4.55 0.793 8 :2@N6_:1@C2 83142 0.937 4.3 0.908 9 :2@N1_:1@N1 83031 0.936 4.53 0.78 10 :2@C5_:1@C6 82985 0.935 5.04 0.712 11 :2@C6_:1@C2 82566 0.93 4.61 0.771 12 :2@C8_:1@N1 82134 0.926 5.67 0.637 13 :2@C5_:1@C2 82087 0.925 5.11 0.705 14 :2@N6_:1@O2 81758 0.921 4.53 1.07 15 :2@N1_:1@C6 81475 0.918 4.73 0.782 16 :2@C6_:1@O2 80988 0.913 4.75 0.814 17 :2@N7_:1@C6 80938 0.912 5.41 0.747 18 :2@C5_:1@O2 80546 0.908 5.13 0.775 19 :2@C2_:1@N1 80475 0.907 5.05 0.753 20 :2@N6_:1@C5 80203 0.904 4.61 0.899 21 :2@N9_:1@N1 80149 0.903 5.85 0.536 22 :2@N6_:1@N3 80094 0.903 4.62 0.872 23 :2@N7_:1@C2 80040 0.902 5.41 0.853 24 :2@N1_:1@C2 79722 0.898 4.81 0.837 25 :2@N3_:1@N1 79437 0.895 5.44 0.644 26 :2@C4_:1@C6 79411 0.895 5.62 0.585 27 :2@N6_:1@C4 79036 0.891 4.77 0.825 28 :2@C2_:1@C6 78911 0.889 5.32 0.728 29 :2@C6_:1@C5 78771 0.888 5.08 0.751 30 :2@C6_:1@N3 78156 0.881 5.15 0.708 31 :2@N1_:1@O2 78077 0.88 4.96 0.939 32 :2@N1_:1@C5 77363 0.872 5.22 0.759 33 :2@N7_:1@O2 77033 0.868 5.29 1.1 34 :2@C6_:1@C4 76565 0.863 5.36 0.69 35 :2@C4_:1@O2 76540 0.863 5.71 0.563 36 :2@C4_:1@C2 76511 0.862 5.72 0.552 37 :2@N3_:1@C6 76195 0.859 5.79 0.605 38 :2@C2_:1@C2 75846 0.855 5.42 0.854 39 :2@N1_:1@N3 75455 0.85 5.3 0.793 40 :2@N1_:1@C4 74348 0.838 5.49 0.735 41 :2@C5_:1@C5 74016 0.834 5.73 0.644 42 :2@C2_:1@O2 73167 0.825 5.45 1.02 43 :2@C5_:1@N3 72562 0.818 5.8 0.593 44 :2@N6_:1@N4 72548 0.818 5.4 0.766 45 :2@N3_:1@C2 71964 0.811 5.9 0.685 46 :2@C8_:1@C6 71602 0.807 6.06 0.611 47 :2@N3_:1@O2 69911 0.788 5.86 0.789 48 :2@C2_:1@C5 68609 0.773 5.89 0.671 49 :2@N9_:1@C6 68250 0.769 6.23 0.492 50 :2@C5_:1@C4 66891 0.754 6.04 0.559 51 :2@C8_:1@C2 65446 0.737 6.01 0.675 52 :2@C2_:1@N3 62989 0.71 5.94 0.775 53 :2@C6_:1@N4 62154 0.7 6.03 0.585 54 :2@N7_:1@N3 61444 0.692 5.99 0.68 55 :2@C8_:1@O2 61177 0.689 5.76 0.844 56 :2@C4_:1@C5 57780 0.651 6.29 0.475 57 :2@N1_:1@N4 57386 0.647 6.07 0.636 58 :2@C2_:1@C4 56864 0.641 6.12 0.652 59 :2@N3_:1@C5 49520 0.558 6.35 0.504 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 88741, 'v_base2' size 88741, output size 88741 TIME: Analyses took 0.0075 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 88741 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 88741 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 88741 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 88741 COM "COM" (double, distance), size is 88741 v_base2 "v_base2" (vector, vector), size is 88741 v_base1 "v_base1" (vector, vector), size is 88741 normalangle "normalangle" (double), size is 88741 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0020 s ( 0.23%) TIME: Trajectory Process : 0.8649 s ( 98.88%) TIME: Action Post : 0.0002 s ( 0.02%) TIME: Analysis : 0.0075 s ( 0.86%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 0.8747 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: 1.1272 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.