CPPTRAJ: Trajectory Analysis. V14.09 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ Reading '../../prot.parm7' as Amber Topology INPUT: Reading Input from STDIN [trajin /home/leexa/Desktop/MDM2_apo/run1/comb_forwaterview_netcdf.mdcrd 2501 10000] Reading '/home/leexa/Desktop/MDM2_apo/run1/comb_forwaterview_netcdf.mdcrd' as Amber NetCDF [hbond out hb.out :2,3,27,28,31,32,34,35,38,39,44,47,48,49,50,52,68,70,71,73,76,77,80,81 angle 120 dist 3.5 series avgout avgout_1909.out printatomnum nointramol solventdonor :WAT solventacceptor :WAT ] HBOND: Searching for Hbond donors/acceptors in region specified by :2,3,27,28,31,32,34,35,38,39,44,47,48,49,50,52,68,70,71,73,76,77,80,81 Only looking for intermolecular hydrogen bonds. Will search for hbonds between solute and solvent donors in [:WAT] Will search for hbonds between solute and solvent acceptors in [:WAT] Distance cutoff = 3.500, Angle Cutoff = 120.000 Dumping # Hbond v time results to hb.out Dumping Hbond avgs to avgout_1909.out Dumping solute-solvent hbond avgs to avgout_1909.out Dumping solvent bridging info to avgout_1909.out Atom numbers will be written to output. Time series data for each hbond will be saved for analysis. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: '../../prot.parm7', 12635 atoms, 3816 res, box: Orthogonal, 3730 mol, 3724 solvent, 7500 frames INPUT TRAJECTORIES: 0: 'comb_forwaterview_netcdf.mdcrd' is a NetCDF AMBER trajectory, Parm ../../prot.parm7 (Orthogonal box) (reading 7500 of 10000) Coordinate processing will occur on 7500 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '../../prot.parm7' (1 actions): 0: [hbond out hb.out :2,3,27,28,31,32,34,35,38,39,44,47,48,49,50,52,68,70,71,73,76,77,80,81 angle 120 dist 3.5 series avgout avgout_1909.out printatomnum nointramol solventdonor :WAT solventacceptor :WAT ] Set up 65 acceptors: Set up 43 donors: Set up 11172 solvent acceptors Set up 7448 solvent donors Imaging off. ----- comb_forwaterview_netcdf.mdcrd (2501-10000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 7500 frames and processed 7500 frames. TIME: Trajectory processing: 60.5053 s TIME: Avg. throughput= 123.9561 frames / second. ACTION OUTPUT: DATASETS: 103 data sets: HB_00000[UU] "HB_00000[UU]" (integer), size is 7500 HB_00000[UV] "HB_00000[UV]" (integer), size is 7500 HB_00000[Bridge] "HB_00000[Bridge]" (integer), size is 7500 HB_00000[ID] "HB_00000[ID]" (string), size is 7500 HB_00000[solventhb]:7 "GLU_2@H-V" (integer), size is 7500 HB_00000[solventhb]:32 "THR_3@HG1-V" (integer), size is 7500 HB_00000[solventhb]:428 "MET_27@H-V" (integer), size is 7500 HB_00000[solventhb]:445 "LYS_28@H-V" (integer), size is 7500 HB_00000[solventhb]:461 "LYS_28@HZ1-V" (integer), size is 7500 HB_00000[solventhb]:462 "LYS_28@HZ2-V" (integer), size is 7500 HB_00000[solventhb]:463 "LYS_28@HZ3-V" (integer), size is 7500 HB_00000[solventhb]:750 "TYR_44@HH-V" (integer), size is 7500 HB_00000[solventhb]:785 "LYS_47@H-V" (integer), size is 7500 HB_00000[solventhb]:801 "LYS_47@HZ1-V" (integer), size is 7500 HB_00000[solventhb]:802 "LYS_47@HZ2-V" (integer), size is 7500 HB_00000[solventhb]:803 "LYS_47@HZ3-V" (integer), size is 7500 HB_00000[solventhb]:819 "GLN_48@HE21-V" (integer), size is 7500 HB_00000[solventhb]:820 "GLN_48@HE22-V" (integer), size is 7500 HB_00000[solventhb]:824 "GLN_49@H-V" (integer), size is 7500 HB_00000[solventhb]:836 "GLN_49@HE21-V" (integer), size is 7500 HB_00000[solventhb]:837 "GLN_49@HE22-V" (integer), size is 7500 HB_00000[solventhb]:852 "HIE_50@HE2-V" (integer), size is 7500 HB_00000[solventhb]:1169 "LYS_71@HZ1-V" (integer), size is 7500 HB_00000[solventhb]:1171 "LYS_71@HZ3-V" (integer), size is 7500 HB_00000[solventhb]:1190 "HIE_73@H-V" (integer), size is 7500 HB_00000[solventhb]:1201 "HIE_73@HE2-V" (integer), size is 7500 HB_00000[solventhb]:1285 "TYR_77@HH-V" (integer), size is 7500 HB_00000[solventhb]:1356 "TYR_81@HH-V" (integer), size is 7500 HB_00000[solventhb]:31 "THR_3@OG1-V" (integer), size is 7500 HB_00000[solventhb]:756 "TYR_44@O-V" (integer), size is 7500 HB_00000[solventhb]:1355 "TYR_81@OH-V" (integer), size is 7500 HB_00000[solventhb]:817 "GLN_48@OE1-V" (integer), size is 7500 HB_00000[solventhb]:18 "GLU_2@OE2-V" (integer), size is 7500 HB_00000[solventhb]:582 "GLY_35@O-V" (integer), size is 7500 HB_00000[solventhb]:640 "MET_39@N-V" (integer), size is 7500 HB_00000[solventhb]:20 "GLU_2@O-V" (integer), size is 7500 HB_00000[solventhb]:1362 "TYR_81@O-V" (integer), size is 7500 HB_00000[solventhb]:17 "GLU_2@OE1-V" (integer), size is 7500 HB_00000[solventhb]:805 "LYS_47@O-V" (integer), size is 7500 HB_00000[solventhb]:834 "GLN_49@OE1-V" (integer), size is 7500 HB_00000[solventhb]:656 "MET_39@O-V" (integer), size is 7500 HB_00000[solventhb]:1151 "VAL_70@O-V" (integer), size is 7500 HB_00000[solventhb]:535 "PHE_32@O-V" (integer), size is 7500 HB_00000[solventhb]:1173 "LYS_71@O-V" (integer), size is 7500 HB_00000[solventhb]:1197 "HIE_73@ND1-V" (integer), size is 7500 HB_00000[solventhb]:839 "GLN_49@O-V" (integer), size is 7500 HB_00000[solventhb]:515 "LEU_31@O-V" (integer), size is 7500 HB_00000[solventhb]:34 "THR_3@O-V" (integer), size is 7500 HB_00000[solventhb]:1205 "HIE_73@O-V" (integer), size is 7500 HB_00000[solventhb]:641 "MET_39@H-V" (integer), size is 7500 HB_00000[solventhb]:1170 "LYS_71@HZ2-V" (integer), size is 7500 HB_00000[solventhb]:1284 "TYR_77@OH-V" (integer), size is 7500 HB_00000[solventhb]:465 "LYS_28@O-V" (integer), size is 7500 HB_00000[solventhb]:22 "THR_3@H-V" (integer), size is 7500 HB_00000[solventhb]:818 "GLN_48@NE2-V" (integer), size is 7500 HB_00000[solventhb]:807 "GLN_48@H-V" (integer), size is 7500 HB_00000[solventhb]:1105 "PHE_68@N-V" (integer), size is 7500 HB_00000[solventhb]:835 "GLN_49@NE2-V" (integer), size is 7500 HB_00000[solventhb]:577 "GLY_35@H-V" (integer), size is 7500 HB_00000[solventhb]:841 "HIE_50@H-V" (integer), size is 7500 HB_00000[solventhb]:1200 "HIE_73@NE2-V" (integer), size is 7500 HB_00000[solventhb]:749 "TYR_44@OH-V" (integer), size is 7500 HB_00000[solventhb]:806 "GLN_48@N-V" (integer), size is 7500 HB_00000[solventhb]:856 "HIE_50@O-V" (integer), size is 7500 HB_00000[solventhb]:517 "PHE_32@H-V" (integer), size is 7500 HB_00000[solventhb]:576 "GLY_35@N-V" (integer), size is 7500 HB_00000[solventhb]:6 "GLU_2@N-V" (integer), size is 7500 HB_00000[solventhb]:1291 "TYR_77@O-V" (integer), size is 7500 HB_00000[solventhb]:784 "LYS_47@N-V" (integer), size is 7500 HB_00000[solventhb]:737 "TYR_44@H-V" (integer), size is 7500 HB_00000[solventhb]:516 "PHE_32@N-V" (integer), size is 7500 HB_00000[solventhb]:1153 "LYS_71@H-V" (integer), size is 7500 HB_00000[solventhb]:851 "HIE_50@NE2-V" (integer), size is 7500 HB_00000[solventhb]:848 "HIE_50@ND1-V" (integer), size is 7500 HB_00000[solventhb]:21 "THR_3@N-V" (integer), size is 7500 HB_00000[solventhb]:1189 "HIE_73@N-V" (integer), size is 7500 HB_00000[solventhb]:444 "LYS_28@N-V" (integer), size is 7500 HB_00000[solventhb]:736 "TYR_44@N-V" (integer), size is 7500 HB_00000[solventhb]:876 "VAL_52@N-V" (integer), size is 7500 HB_00000[solventhb]:1124 "PHE_68@O-V" (integer), size is 7500 HB_00000[solventhb]:1253 "ILE_76@H-V" (integer), size is 7500 HB_00000[solventhb]:1272 "TYR_77@H-V" (integer), size is 7500 HB_00000[solventhb]:840 "HIE_50@N-V" (integer), size is 7500 HB_00000[solventhb]:1168 "LYS_71@NZ-V" (integer), size is 7500 HB_00000[solventhb]:800 "LYS_47@NZ-V" (integer), size is 7500 HB_00000[solventhb]:427 "MET_27@N-V" (integer), size is 7500 HB_00000[solventhb]:460 "LYS_28@NZ-V" (integer), size is 7500 HB_00000[solventhb]:891 "VAL_52@O-V" (integer), size is 7500 HB_00000[solventhb]:443 "MET_27@O-V" (integer), size is 7500 HB_00000[solventhb]:823 "GLN_49@N-V" (integer), size is 7500 HB_00000[solventhb]:1270 "ILE_76@O-V" (integer), size is 7500 HB_00000[solventhb]:1271 "TYR_77@N-V" (integer), size is 7500 HB_00000[solventhb]:877 "VAL_52@H-V" (integer), size is 7500 HB_00000[solventhb]:822 "GLN_48@O-V" (integer), size is 7500 HB_00000[solventhb]:1343 "TYR_81@H-V" (integer), size is 7500 HB_00000[solventhb]:1152 "LYS_71@N-V" (integer), size is 7500 HB_00000[solventhb]:1136 "VAL_70@N-V" (integer), size is 7500 HB_00000[solventhb]:1341 "ILE_80@O-V" (integer), size is 7500 HB_00000[solventhb]:1137 "VAL_70@H-V" (integer), size is 7500 HB_00000[solventhb]:1342 "TYR_81@N-V" (integer), size is 7500 HB_00000[solventhb]:1106 "PHE_68@H-V" (integer), size is 7500 HB_00000[solventhb]:1252 "ILE_76@N-V" (integer), size is 7500 HB_00000[solventhb]:622 "ILE_38@H-V" (integer), size is 7500 DATAFILES: hb.out (Standard Data File): HB_00000[UU] HB_00000[UV] HB_00000[Bridge] HB_00000[ID] ---------- RUN END --------------------------------------------------- TIME: Total execution time: 60.6080 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.