CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/03/16 12:28:10 | Available memory: 1.227 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 202878 of 202878) Coordinate processing will occur on 202878 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 (1-202878, 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 202878 frames and processed 202878 frames. TIME: Avg. throughput= 88954.3854 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00002 #Res1 #Res2 TotalFrac Contacts 1 2 74.4374 84 # Contact Nframes Frac. Avg Stdev 1 :1@N9_:2@C5 199972 0.986 4.66 0.678 2 :1@C4_:2@C5 199347 0.983 4.62 0.724 3 :1@C4_:2@C6 198165 0.977 4.27 0.792 4 :1@C4_:2@O6 197704 0.974 4.38 0.832 5 :1@N9_:2@N7 197470 0.973 5.02 0.784 6 :1@N9_:2@N9 197406 0.973 5.43 0.579 7 :1@N9_:2@C4 196500 0.969 4.87 0.583 8 :1@N9_:2@C6 195964 0.966 4.54 0.699 9 :1@C4_:2@C4 195958 0.966 5.03 0.66 10 :1@N3_:2@C5 195584 0.964 4.68 0.763 11 :1@N3_:2@C6 195451 0.963 4.35 0.819 12 :1@C4_:2@N7 194760 0.96 5.04 0.792 13 :1@N3_:2@O6 194731 0.96 4.46 0.865 14 :1@N9_:2@O6 194107 0.957 4.83 0.768 15 :1@N9_:2@C8 193722 0.955 5.4 0.722 16 :1@C5_:2@O6 192774 0.95 4.2 0.972 17 :1@C5_:2@C6 192444 0.949 4.33 0.87 18 :1@N9_:2@N1 192228 0.948 4.61 0.769 19 :1@N9_:2@N3 191841 0.946 4.98 0.684 20 :1@N3_:2@C4 191802 0.945 5.08 0.667 21 :1@C4_:2@N1 191417 0.944 4.3 0.786 22 :1@C5_:2@C5 191253 0.943 4.93 0.823 23 :1@N3_:2@N1 190814 0.941 4.4 0.921 24 :1@C8_:2@C6 189742 0.935 4.7 0.847 25 :1@N9_:2@C2 189670 0.935 4.79 0.795 26 :1@C6_:2@O6 189646 0.935 4.18 1.1 27 :1@C8_:2@C5 189283 0.933 4.91 0.804 28 :1@C8_:2@C4 188674 0.93 5.23 0.704 29 :1@C5_:2@N1 187712 0.925 4.37 0.845 30 :1@C4_:2@N9 187672 0.925 5.68 0.583 31 :1@N3_:2@N7 187538 0.924 5.03 0.859 32 :1@C8_:2@N1 187476 0.924 4.76 0.943 33 :1@C2_:2@C6 187176 0.923 4.43 0.833 34 :1@C4_:2@C2 187048 0.922 4.69 0.752 35 :1@C4_:2@N3 186241 0.918 5.08 0.636 36 :1@N3_:2@N3 186197 0.918 5.17 0.761 37 :1@C2_:2@N1 186129 0.917 4.5 0.975 38 :1@C2_:2@O6 186041 0.917 4.25 0.906 39 :1@N7_:2@C6 185963 0.917 4.61 0.855 40 :1@N7_:2@N1 185850 0.916 4.68 0.995 41 :1@C6_:2@C6 185804 0.916 4.54 0.92 42 :1@N1_:2@O6 185612 0.915 4.18 0.992 43 :1@N3_:2@C2 184474 0.909 4.75 0.905 44 :1@N1_:2@C6 183855 0.906 4.55 0.848 45 :1@C8_:2@N3 183146 0.903 5.3 0.839 46 :1@C8_:2@C2 182914 0.902 5 1 47 :1@C8_:2@O6 182114 0.898 4.78 0.901 48 :1@C5_:2@C4 181142 0.893 5.43 0.66 49 :1@C2_:2@C5 180804 0.891 4.96 0.741 50 :1@N7_:2@O6 180775 0.891 4.44 0.891 51 :1@C6_:2@N1 180700 0.891 4.55 0.779 52 :1@N1_:2@N1 180551 0.89 4.6 0.83 53 :1@C5_:2@C2 180512 0.89 4.92 0.772 54 :1@N3_:2@N9 180280 0.889 5.69 0.614 55 :1@N3_:2@C8 176448 0.87 5.55 0.795 56 :1@N7_:2@C2 176261 0.869 5.1 1.01 57 :1@C2_:2@C2 175976 0.867 5.03 0.942 58 :1@C4_:2@N2 175773 0.866 5.06 0.818 59 :1@N2_:2@C6 175344 0.864 4.79 0.846 60 :1@C5_:2@N3 174919 0.862 5.48 0.646 61 :1@C2_:2@C4 174918 0.862 5.53 0.624 62 :1@N2_:2@O6 174414 0.86 4.57 0.944 63 :1@N9_:2@N2 174234 0.859 5.14 0.876 64 :1@N2_:2@N1 173485 0.855 4.84 1.08 65 :1@O6_:2@N1 172433 0.85 5.05 0.805 66 :1@C6_:2@C2 172167 0.849 5.3 0.68 67 :1@N1_:2@C2 169902 0.837 5.31 0.745 68 :1@C2_:2@N7 169806 0.837 5.3 0.931 69 :1@C2_:2@N3 169030 0.833 5.6 0.723 70 :1@C5_:2@N2 168414 0.83 5.21 0.875 71 :1@N3_:2@N2 168254 0.829 5.01 0.997 72 :1@N2_:2@C5 168104 0.829 5.3 0.806 73 :1@N7_:2@N3 167242 0.824 5.57 0.819 74 :1@C6_:2@N2 159263 0.785 5.52 0.778 75 :1@C8_:2@N2 154083 0.759 5.06 1.13 76 :1@N2_:2@C4 153990 0.759 5.82 0.673 77 :1@N1_:2@N2 153399 0.756 5.46 0.889 78 :1@C2_:2@N2 152417 0.751 5.09 1.06 79 :1@N2_:2@C2 151771 0.748 5.16 1.04 80 :1@N7_:2@N2 145564 0.717 5.05 1.09 81 :1@N2_:2@N7 143355 0.707 5.39 1.05 82 :1@N2_:2@N3 136520 0.673 5.7 0.746 83 :1@O6_:2@N2 131502 0.648 5.84 0.746 84 :1@N2_:2@N2 120558 0.594 4.81 1.11 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] 'v_base1' size 202878, 'v_base2' size 202878, output size 202878 TIME: Analyses took 0.0145 seconds. DATASETS (8 total): RMSD_00001 "RMSD_00001" (double, rms), size is 202878 Contacts_00002[native] "Contacts_00002[native]" (integer), size is 202878 Contacts_00002[nonnative] "Contacts_00002[nonnative]" (integer), size is 202878 Contacts_00002[mindist] "Contacts_00002[mindist]" (double), size is 202878 COM "COM" (double, distance), size is 202878 v_base1 "v_base1" (vector, vector), size is 202878 v_base2 "v_base2" (vector, vector), size is 202878 normalangle "normalangle" (double), size is 202878 DATAFILES (2 total): STDOUT (Native Contacts) STDOUT (Contact Res Pairs) RUN TIMING: TIME: Init : 0.0011 s ( 0.05%) TIME: Trajectory Process : 2.2807 s ( 99.31%) TIME: Action Post : 0.0002 s ( 0.01%) TIME: Analysis : 0.0145 s ( 0.63%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0000 s ( 0.00%) TIME: Run Total 2.2965 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: 2.8227 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.