CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/05/16 18:46:00 | Available memory: 1.914 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.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,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@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 :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] VECTOR: Type CorrPlane, mask [:2@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.c1' is a NetCDF AMBER trajectory, Parm noWAt.topo.hmr (Orthogonal box) (reading 111268 of 111268) Coordinate processing will occur on 111268 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 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C6,C5,C4,N4,N3,C2,O2 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 8 potential contact sites for ':2@N1,C6,C5,C4,N4,N3,C2,O2' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C6,H6,C5,H5,C4,N4,H41,H42,N3,C2,O2 (12 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :2@N1,C6,C5,C4,N4,N3,C2,O2 corrplane] Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. ----- ctraj.c1 (1-111268, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C6,C5,C4,N4,N3,C2,O2] corresponds to 8 atoms. Setup 79 native contacts: Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C4' Atom ':1@N9' to ':2@N4' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@O2' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C4' Atom ':1@C8' to ':2@N4' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C2' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@C5' Atom ':1@N7' to ':2@C4' Atom ':1@N7' to ':2@N4' Atom ':1@N7' to ':2@N3' Atom ':1@N7' to ':2@C2' Atom ':1@N7' 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@C4' Atom ':1@C5' to ':2@N4' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C2' Atom ':1@C5' 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@C4' Atom ':1@C6' to ':2@N4' Atom ':1@C6' to ':2@N3' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@O2' Atom ':1@N6' to ':2@N1' Atom ':1@N6' to ':2@C6' Atom ':1@N6' to ':2@C5' Atom ':1@N6' to ':2@C4' Atom ':1@N6' to ':2@N4' Atom ':1@N6' to ':2@N3' Atom ':1@N6' to ':2@C2' Atom ':1@N6' to ':2@O2' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C4' Atom ':1@N1' to ':2@N4' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C2' Atom ':1@N1' 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@C4' Atom ':1@C2' to ':2@N4' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C2' Atom ':1@C2' 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@C4' Atom ':1@N3' to ':2@N4' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C2' Atom ':1@N3' 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@C4' Atom ':1@C4' to ':2@N4' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@O2' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 111268 frames and processed 111268 frames. TIME: Avg. throughput= 71536.8582 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 75.2907 79 # Contact Nframes Frac. Avg Stdev 1 :1@C4_:2@C4 111052 0.998 4.34 0.651 2 :1@C4_:2@C6 110956 0.997 4.38 0.637 3 :1@C5_:2@C4 110922 0.997 4.2 0.812 4 :1@C4_:2@C5 110803 0.996 4.13 0.699 5 :1@N9_:2@C6 110758 0.995 4.77 0.622 6 :1@C4_:2@N1 110551 0.994 4.77 0.534 7 :1@C5_:2@C5 110546 0.994 4.34 0.804 8 :1@C4_:2@N3 110436 0.993 4.72 0.691 9 :1@N3_:2@N1 110341 0.992 4.39 0.617 10 :1@N3_:2@C4 110270 0.991 4.49 0.632 11 :1@N3_:2@C6 110230 0.991 4.17 0.715 12 :1@N9_:2@C5 110199 0.99 4.43 0.743 13 :1@N3_:2@N3 110177 0.99 4.7 0.653 14 :1@N3_:2@C2 110145 0.99 4.65 0.634 15 :1@N3_:2@C5 110104 0.99 4.21 0.705 16 :1@C6_:2@C4 110096 0.989 4.16 0.788 17 :1@C6_:2@N3 109891 0.988 4.16 0.756 18 :1@C4_:2@C2 109823 0.987 4.91 0.651 19 :1@C4_:2@N4 109796 0.987 4.67 0.714 20 :1@C2_:2@C2 109704 0.986 4.27 0.724 21 :1@N1_:2@N3 109698 0.986 4.1 0.729 22 :1@C2_:2@C6 109504 0.984 4.39 0.793 23 :1@C2_:2@N1 109489 0.984 4.29 0.725 24 :1@C2_:2@N3 109487 0.984 4.33 0.721 25 :1@C5_:2@N3 109399 0.983 4.47 0.792 26 :1@C5_:2@C6 109357 0.983 4.78 0.652 27 :1@C2_:2@C4 109144 0.981 4.38 0.742 28 :1@C2_:2@C5 109115 0.981 4.43 0.804 29 :1@N9_:2@N1 109108 0.981 5.39 0.539 30 :1@C6_:2@C5 109107 0.981 4.59 0.796 31 :1@N1_:2@C4 109095 0.98 4.27 0.759 32 :1@N1_:2@C2 109062 0.98 4.23 0.693 33 :1@N9_:2@C4 108972 0.979 4.83 0.737 34 :1@C6_:2@N4 108744 0.977 4.27 0.868 35 :1@C5_:2@N4 108490 0.975 4.24 0.867 36 :1@N3_:2@N4 108444 0.975 5.02 0.683 37 :1@N1_:2@C6 108198 0.972 4.8 0.733 38 :1@N1_:2@C5 108153 0.972 4.64 0.795 39 :1@N1_:2@N1 108031 0.971 4.58 0.631 40 :1@C6_:2@C6 107927 0.97 4.96 0.664 41 :1@C6_:2@C2 107763 0.968 4.5 0.643 42 :1@C2_:2@O2 107753 0.968 4.66 0.769 43 :1@C8_:2@C5 107467 0.966 4.73 0.845 44 :1@C5_:2@N1 107430 0.966 5.01 0.568 45 :1@C6_:2@N1 107200 0.963 4.91 0.561 46 :1@N3_:2@O2 107111 0.963 5.24 0.719 47 :1@C5_:2@C2 107073 0.962 4.84 0.698 48 :1@N6_:2@C4 107042 0.962 4.53 0.841 49 :1@N6_:2@N3 107000 0.962 4.38 0.765 50 :1@N7_:2@C5 106828 0.96 4.71 0.841 51 :1@N1_:2@O2 106772 0.96 4.49 0.726 52 :1@C8_:2@C6 106685 0.959 5.29 0.673 53 :1@N1_:2@N4 106621 0.958 4.58 0.81 54 :1@C2_:2@N4 105967 0.952 4.87 0.801 55 :1@N6_:2@C2 105239 0.946 4.89 0.673 56 :1@N6_:2@N4 105122 0.945 4.39 0.941 57 :1@C6_:2@O2 105038 0.944 4.88 0.733 58 :1@N7_:2@C6 105028 0.944 5.32 0.669 59 :1@N9_:2@N3 104989 0.944 5.38 0.739 60 :1@N7_:2@C4 104696 0.941 4.51 0.853 61 :1@N9_:2@C2 104424 0.938 5.63 0.691 62 :1@N9_:2@N4 104244 0.937 4.97 0.756 63 :1@C4_:2@O2 103523 0.93 5.54 0.771 64 :1@C8_:2@C4 103352 0.929 4.83 0.836 65 :1@N6_:2@C5 103044 0.926 5.18 0.772 66 :1@N6_:2@N1 102983 0.926 5.53 0.602 67 :1@N6_:2@O2 102477 0.921 5.1 0.783 68 :1@N7_:2@N4 101887 0.916 4.25 0.909 69 :1@N7_:2@N3 101651 0.914 4.96 0.869 70 :1@C5_:2@O2 101589 0.913 5.39 0.824 71 :1@N6_:2@C6 100564 0.904 5.65 0.634 72 :1@N7_:2@N1 99913 0.898 5.67 0.697 73 :1@C8_:2@N4 99677 0.896 4.66 0.885 74 :1@C8_:2@N1 99148 0.891 5.8 0.664 75 :1@N7_:2@C2 98624 0.886 5.49 0.837 76 :1@C8_:2@N3 96911 0.871 5.39 0.848 77 :1@C8_:2@C2 91327 0.821 5.8 0.81 78 :1@N7_:2@O2 74936 0.673 5.82 0.96 79 :1@N9_:2@O2 73024 0.656 6.08 0.857 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 111268, 'v_base2' size 111268, output size 111268 TIME: Analyses took 0.0158 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 111268 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 111268 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 111268 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 111268 COM "COM" (double, distance), size is 111268 v_base1 "v_base1" (vector, vector), size is 111268 v_base2 "v_base2" (vector, vector), size is 111268 normalangle "normalangle" (double), size is 111268 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0027 s ( 0.17%) TIME: Trajectory Process : 1.5554 s ( 98.81%) TIME: Action Post : 0.0002 s ( 0.02%) TIME: Analysis : 0.0158 s ( 1.00%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 1.5742 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: 1.9328 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.