CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:32:21 | Available memory: 1.233 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 :1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Mask2=':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9', 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,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] [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] [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, 67 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 204603 of 204603) Coordinate processing will occur on 204603 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*](43) Reference mask: [:1,2&!@H*](43) 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,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 :2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9 mindist] Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. 11 potential contact sites for ':1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' 11 potential contact sites for ':2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6] :1@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N2,H21,H22,N7,C8,H8,N9,O6 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6 corrplane] Mask [:1@N1,C2,N3,C4,C5,C6,N2,N7,C8,N9,O6] corresponds to 11 atoms. 6: [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. ----- ctraj.c0 (1-204603, 1) ----- Using first frame to determine native contacts. Mask [:1@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Mask [:2@N1,N2,C2,N3,C4,C5,C6,O6,N7,C8,N9] corresponds to 11 atoms. Setup 84 native contacts: Atom ':1@N9' to ':2@N9' Atom ':1@N9' to ':2@C8' Atom ':1@N9' to ':2@N7' Atom ':1@N9' to ':2@C5' Atom ':1@N9' to ':2@C6' Atom ':1@N9' to ':2@O6' Atom ':1@N9' to ':2@N1' Atom ':1@N9' to ':2@C2' Atom ':1@N9' to ':2@N2' Atom ':1@N9' to ':2@N3' Atom ':1@N9' to ':2@C4' Atom ':1@C8' to ':2@C5' Atom ':1@C8' to ':2@C6' Atom ':1@C8' to ':2@O6' Atom ':1@C8' to ':2@N1' Atom ':1@C8' to ':2@C2' Atom ':1@C8' to ':2@N2' Atom ':1@C8' to ':2@N3' Atom ':1@C8' to ':2@C4' Atom ':1@N7' to ':2@C6' Atom ':1@N7' to ':2@O6' Atom ':1@N7' to ':2@N1' Atom ':1@N7' to ':2@C2' Atom ':1@N7' to ':2@N2' Atom ':1@N7' to ':2@N3' Atom ':1@C5' to ':2@C5' Atom ':1@C5' to ':2@C6' Atom ':1@C5' to ':2@O6' Atom ':1@C5' to ':2@N1' Atom ':1@C5' to ':2@C2' Atom ':1@C5' to ':2@N2' Atom ':1@C5' to ':2@N3' Atom ':1@C5' to ':2@C4' Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@O6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@C6' to ':2@N2' Atom ':1@O6' to ':2@N1' Atom ':1@O6' to ':2@N2' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@O6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N2' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@O6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N2' to ':2@N7' Atom ':1@N2' to ':2@C5' Atom ':1@N2' to ':2@C6' Atom ':1@N2' to ':2@O6' Atom ':1@N2' to ':2@N1' Atom ':1@N2' to ':2@C2' Atom ':1@N2' to ':2@N2' Atom ':1@N2' to ':2@N3' Atom ':1@N2' to ':2@C4' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@O6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@O6' Atom ':1@C4' to ':2@N1' Atom ':1@C4' to ':2@C2' Atom ':1@C4' to ':2@N2' Atom ':1@C4' to ':2@N3' Atom ':1@C4' to ':2@C4' 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 204603 frames and processed 204603 frames. TIME: Avg. throughput= 81743.1736 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 74.6486 84 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 200113 0.978 4.64 0.669 2 :1@C4_:2@C5 199629 0.976 4.58 0.7 3 :1@C4_:2@C6 198860 0.972 4.28 0.764 4 :1@C4_:2@O6 198330 0.969 4.41 0.836 5 :1@N9_:2@N7 198110 0.968 4.94 0.764 6 :1@N9_:2@N9 197797 0.967 5.34 0.61 7 :1@N3_:2@C6 197666 0.966 4.39 0.803 8 :1@N3_:2@C5 197290 0.964 4.69 0.734 9 :1@N9_:2@C4 197258 0.964 4.85 0.569 10 :1@C4_:2@C4 197198 0.964 4.98 0.641 11 :1@N3_:2@O6 196752 0.962 4.5 0.859 12 :1@N9_:2@C6 196583 0.961 4.59 0.761 13 :1@C4_:2@N7 195075 0.953 4.97 0.822 14 :1@N9_:2@C8 194798 0.952 5.29 0.749 15 :1@N3_:2@C4 194402 0.95 5.08 0.652 16 :1@N3_:2@N1 194202 0.949 4.45 0.957 17 :1@C4_:2@N1 194118 0.949 4.37 0.808 18 :1@C5_:2@C6 194086 0.949 4.32 0.841 19 :1@C5_:2@O6 193880 0.948 4.22 0.97 20 :1@N9_:2@N3 193545 0.946 5.05 0.685 21 :1@N9_:2@O6 192709 0.942 4.86 0.817 22 :1@C5_:2@C5 192606 0.941 4.85 0.839 23 :1@C6_:2@O6 192016 0.938 4.19 1.07 24 :1@N9_:2@N1 191385 0.935 4.71 0.841 25 :1@C5_:2@N1 191228 0.935 4.41 0.821 26 :1@C4_:2@C2 190797 0.933 4.76 0.767 27 :1@C2_:2@C6 190469 0.931 4.45 0.817 28 :1@C8_:2@C5 190254 0.93 4.87 0.789 29 :1@C8_:2@C6 190121 0.929 4.75 0.895 30 :1@N9_:2@C2 190110 0.929 4.91 0.84 31 :1@C4_:2@N3 190102 0.929 5.1 0.62 32 :1@C2_:2@N1 190099 0.929 4.5 0.978 33 :1@C8_:2@C4 189945 0.928 5.19 0.713 34 :1@N3_:2@N3 189656 0.927 5.19 0.78 35 :1@C6_:2@C6 189269 0.925 4.51 0.915 36 :1@C4_:2@N9 189148 0.924 5.59 0.667 37 :1@C2_:2@O6 189044 0.924 4.29 0.895 38 :1@N3_:2@N7 188674 0.922 5.03 0.868 39 :1@N1_:2@O6 188445 0.921 4.19 0.968 40 :1@N3_:2@C2 188105 0.919 4.79 0.954 41 :1@N7_:2@N1 187539 0.917 4.76 0.987 42 :1@N1_:2@C6 187133 0.915 4.53 0.846 43 :1@N7_:2@C6 187123 0.915 4.62 0.867 44 :1@C8_:2@N1 186777 0.913 4.88 0.99 45 :1@C6_:2@N1 185323 0.906 4.53 0.779 46 :1@N1_:2@N1 185066 0.905 4.55 0.833 47 :1@C5_:2@C2 185057 0.904 4.95 0.758 48 :1@C5_:2@C4 184326 0.901 5.34 0.74 49 :1@C8_:2@N3 184147 0.9 5.33 0.836 50 :1@C2_:2@C5 183664 0.898 4.96 0.735 51 :1@C8_:2@C2 183151 0.895 5.12 1.01 52 :1@N3_:2@N9 182587 0.892 5.68 0.629 53 :1@C2_:2@C2 180727 0.883 5 0.973 54 :1@N7_:2@O6 180638 0.883 4.48 0.945 55 :1@C5_:2@N3 179546 0.878 5.43 0.689 56 :1@N7_:2@C2 178954 0.875 5.17 0.989 57 :1@C8_:2@O6 178787 0.874 4.79 0.935 58 :1@N2_:2@C6 178661 0.873 4.82 0.84 59 :1@C2_:2@C4 178213 0.871 5.51 0.641 60 :1@N3_:2@C8 177809 0.869 5.54 0.827 61 :1@N2_:2@N1 177584 0.868 4.82 1.09 62 :1@N2_:2@O6 177425 0.867 4.61 0.951 63 :1@O6_:2@N1 177155 0.866 4.97 0.87 64 :1@C6_:2@C2 177136 0.866 5.23 0.732 65 :1@C4_:2@N2 176998 0.865 5.14 0.852 66 :1@N1_:2@C2 175142 0.856 5.22 0.78 67 :1@C2_:2@N3 173123 0.846 5.56 0.756 68 :1@C5_:2@N2 172705 0.844 5.28 0.867 69 :1@C2_:2@N7 171174 0.837 5.33 0.943 70 :1@N2_:2@C5 170811 0.835 5.35 0.77 71 :1@N7_:2@N3 170043 0.831 5.53 0.864 72 :1@N9_:2@N2 168208 0.822 5.24 0.874 73 :1@N3_:2@N2 166219 0.812 4.99 1.02 74 :1@C6_:2@N2 164684 0.805 5.46 0.802 75 :1@N1_:2@N2 160014 0.782 5.38 0.912 76 :1@N2_:2@C4 156656 0.766 5.84 0.663 77 :1@C2_:2@N2 154663 0.756 5.02 1.09 78 :1@N2_:2@C2 154480 0.755 5.09 1.07 79 :1@C8_:2@N2 149294 0.73 5.22 1.14 80 :1@N7_:2@N2 146967 0.718 5.2 1.09 81 :1@N2_:2@N7 143559 0.702 5.49 0.993 82 :1@N2_:2@N3 138934 0.679 5.64 0.804 83 :1@O6_:2@N2 137175 0.67 5.68 0.872 84 :1@N2_:2@N2 124085 0.606 4.68 1.08 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 204603, 'v_base2' size 204603, output size 204603 TIME: Analyses took 0.0145 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 204603 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 204603 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 204603 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 204603 COM "COM" (double, distance), size is 204603 v_base1 "v_base1" (vector, vector), size is 204603 v_base2 "v_base2" (vector, vector), size is 204603 normalangle "normalangle" (double), size is 204603 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0009 s ( 0.04%) TIME: Trajectory Process : 2.5030 s ( 99.38%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0145 s ( 0.57%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.5186 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: 3.0497 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.