bezek:~/ng/mm/DockPrep> grid.SunOS -i grid.in UUUUUUU CCCCCCCC SSSSSSS/ FFFFFFFFF UU/ UU/ CC/ CC/ SS/ FF/ FF/ UU/ CCCCCCCC/ SS/ FF/ FF/ UU/ UUUU/ CC/ CC\ SS/ FF/ FF/ UU/ UU/ CC/ CC\ SS/ FF/ FF/ UUUUUUU/ CC/ CC\ SSSSSS/ FFFFFFFFF/ University of California at San Francisco, DOCK 4.0.1 Raj: total.rlim_cur = 2147483647 __________________Job_Information_________________ launch_time Thu Jan 10 11:30:47 2002 host_name bezek.dstc.monash.edu.au memory_limit 2147483647 working_directory /home/rajkumar/ng/mm/DockPrep user_name rajkumar ________________General_Parameters________________ compute_grids yes grid_spacing 0.3 output_molecule yes ________________Scoring_Parameters________________ contact_score yes contact_cutoff_distance 4.5 chemical_score yes energy_score yes energy_cutoff_distance 10 atom_model a attractive_exponent 6 repulsive_exponent 12 distance_dielectric yes dielectric_factor 4 bump_filter yes bump_overlap 0.75 ____________________File_Input____________________ receptor_file ece.mol2 box_file box.pdb vdw_definition_file parameter/vdw.defn chemical_definition_file parameter/chem.defn ____________________File_Output___________________ score_grid_prefix dock_inputs/ece receptor_out_file ece_out.mol2 Reading in coordinates of receptor. CHARGED RESIDUE GLU5 : -1.000 CHARGED RESIDUE ASP19 : -1.000 CHARGED RESIDUE ASP23 : -1.000 CHARGED RESIDUE ASP27 : -1.000 CHARGED RESIDUE LYS38 : 1.000 CHARGED RESIDUE ASP44 : -1.000 CHARGED RESIDUE ARG48 : 1.000 CHARGED RESIDUE GLU57 : -1.000 CHARGED RESIDUE LYS64 : 1.000 CHARGED RESIDUE GLU68 : -1.000 CHARGED RESIDUE GLU76 : -1.000 CHARGED RESIDUE GLU78 : -1.000 CHARGED RESIDUE ARG79 : 1.000 CHARGED RESIDUE LYS80 : 1.000 CHARGED RESIDUE ARG86 : 1.000 CHARGED RESIDUE GLU91 : -1.000 CHARGED RESIDUE ARG93 : 1.000 CHARGED RESIDUE GLU95 : -1.000 CHARGED RESIDUE GLU96 : -1.000 CHARGED RESIDUE ARG98 : 1.000 CHARGED RESIDUE LYS100 : 1.000 CHARGED RESIDUE GLU104 : -1.000 CHARGED RESIDUE GLU107 : -1.000 CHARGED RESIDUE ARG108 : 1.000 CHARGED RESIDUE LYS120 : 1.000 CHARGED RESIDUE ASP121 : -1.000 CHARGED RESIDUE ASP125 : -1.000 CHARGED RESIDUE ARG135 : 1.000 CHARGED RESIDUE ASP147 : -1.000 CHARGED RESIDUE LYS149 : 1.000 CHARGED RESIDUE ASP159 : -1.000 CHARGED RESIDUE ARG168 : 1.000 CHARGED RESIDUE ASP169 : -1.000 CHARGED RESIDUE LYS174 : 1.000 CHARGED RESIDUE GLU176 : -1.000 CHARGED RESIDUE GLU178 : -1.000 CHARGED RESIDUE LYS179 : 1.000 CHARGED RESIDUE LYS193 : 1.000 CHARGED RESIDUE ASP199 : -1.000 CHARGED RESIDUE GLU200 : -1.000 CHARGED RESIDUE GLU201 : -1.000 CHARGED RESIDUE ARG204 : 1.000 CHARGED RESIDUE ASP212 : -1.000 CHARGED RESIDUE GLU214 : -1.000 CHARGED RESIDUE GLU225 : -1.000 CHARGED RESIDUE LYS226 : 1.000 CHARGED RESIDUE ARG227 : 1.000 CHARGED RESIDUE ARG228 : 1.000 CHARGED RESIDUE ASP229 : -1.000 CHARGED RESIDUE GLU230 : -1.000 CHARGED RESIDUE GLU231 : -1.000 CHARGED RESIDUE LYS236 : 1.000 CHARGED RESIDUE GLU241 : -1.000 CHARGED RESIDUE GLU263 : -1.000 CHARGED RESIDUE GLU266 : -1.000 CHARGED RESIDUE GLU268 : -1.000 CHARGED RESIDUE ASP274 : -1.000 CHARGED RESIDUE LYS275 : 1.000 CHARGED RESIDUE GLU276 : -1.000 CHARGED RESIDUE GLU279 : -1.000 CHARGED RESIDUE ASP289 : -1.000 CHARGED RESIDUE ARG290 : 1.000 CHARGED RESIDUE ARG303 : 1.000 CHARGED RESIDUE LYS304 : 1.000 CHARGED RESIDUE ASP310 : -1.000 CHARGED RESIDUE ARG312 : 1.000 CHARGED RESIDUE ASP315 : -1.000 CHARGED RESIDUE ASP317 : -1.000 CHARGED RESIDUE GLU318 : -1.000 CHARGED RESIDUE LYS319 : 1.000 CHARGED RESIDUE GLU322 : -1.000 CHARGED RESIDUE LYS328 : 1.000 CHARGED RESIDUE LYS329 : 1.000 CHARGED RESIDUE ARG334 : 1.000 CHARGED RESIDUE LYS336 : 1.000 CHARGED RESIDUE ASP341 : -1.000 CHARGED RESIDUE GLU343 : -1.000 CHARGED RESIDUE LYS356 : 1.000 CHARGED RESIDUE GLU361 : -1.000 CHARGED RESIDUE ASP362 : -1.000 CHARGED RESIDUE LYS364 : 1.000 CHARGED RESIDUE GLU369 : -1.000 CHARGED RESIDUE GLU373 : -1.000 CHARGED RESIDUE LYS375 : 1.000 CHARGED RESIDUE LYS376 : 1.000 CHARGED RESIDUE GLU379 : -1.000 CHARGED RESIDUE GLU380 : -1.000 CHARGED RESIDUE LYS386 : 1.000 CHARGED RESIDUE ASP389 : -1.000 CHARGED RESIDUE GLU390 : -1.000 CHARGED RESIDUE GLU391 : -1.000 CHARGED RESIDUE ARG393 : 1.000 CHARGED RESIDUE LYS394 : 1.000 CHARGED RESIDUE LYS397 : 1.000 CHARGED RESIDUE GLU398 : -1.000 CHARGED RESIDUE LYS399 : 1.000 CHARGED RESIDUE ASP401 : -1.000 CHARGED RESIDUE ASP415 : -1.000 CHARGED RESIDUE LYS417 : 1.000 CHARGED RESIDUE GLU418 : -1.000 CHARGED RESIDUE ASP420 : -1.000 CHARGED RESIDUE LYS421 : 1.000 CHARGED RESIDUE ASP425 : -1.000 CHARGED RESIDUE ASP431 : -1.000 CHARGED RESIDUE GLU435 : -1.000 CHARGED RESIDUE ARG439 : 1.000 CHARGED RESIDUE ARG446 : 1.000 CHARGED RESIDUE ASP450 : -1.000 CHARGED RESIDUE ARG453 : 1.000 CHARGED RESIDUE LYS454 : 1.000 CHARGED RESIDUE ARG458 : 1.000 CHARGED RESIDUE ASP459 : -1.000 CHARGED RESIDUE LYS476 : 1.000 CHARGED RESIDUE GLU478 : -1.000 CHARGED RESIDUE ARG493 : 1.000 CHARGED RESIDUE LYS497 : 1.000 CHARGED RESIDUE GLU511 : -1.000 CHARGED RESIDUE ASP517 : -1.000 CHARGED RESIDUE ASP518 : -1.000 CHARGED RESIDUE ARG521 : 1.000 CHARGED RESIDUE GLU522 : -1.000 CHARGED RESIDUE ASP524 : -1.000 CHARGED RESIDUE LYS525 : 1.000 CHARGED RESIDUE ASP526 : -1.000 CHARGED RESIDUE ARG530 : 1.000 CHARGED RESIDUE LYS534 : 1.000 CHARGED RESIDUE GLU539 : -1.000 CHARGED RESIDUE LYS542 : 1.000 CHARGED RESIDUE ARG543 : 1.000 CHARGED RESIDUE GLU546 : -1.000 CHARGED RESIDUE GLU550 : -1.000 CHARGED RESIDUE GLU560 : -1.000 CHARGED RESIDUE ARG565 : 1.000 CHARGED RESIDUE GLU570 : -1.000 CHARGED RESIDUE ASP574 : -1.000 CHARGED RESIDUE LYS579 : 1.000 CHARGED RESIDUE ARG583 : 1.000 CHARGED RESIDUE LYS590 : 1.000 CHARGED RESIDUE LYS591 : 1.000 CHARGED RESIDUE GLU595 : -1.000 CHARGED RESIDUE ARG621 : 1.000 CHARGED RESIDUE GLU624 : -1.000 CHARGED RESIDUE GLU628 : -1.000 CHARGED RESIDUE ASP633 : -1.000 CHARGED RESIDUE ARG639 : 1.000 CHARGED RESIDUE ARG641 : 1.000 CHARGED RESIDUE LYS650 : 1.000 CHARGED RESIDUE GLU651 : -1.000 CHARGED RESIDUE GLU654 : -1.000 CHARGED RESIDUE ARG657 : 1.000 CHARGED RESIDUE LYS669 : 1.000 CHARGED RESIDUE GLU671 : -1.000 CHARGED RESIDUE ZN66674 : 2.000 Total charge on **** : -14.000 Writing out processed receptor. Reading in grid box information. Box center of mass : -1.722 2.763 -28.288 Box dimensions : 29.806 24.926 27.460 Number of grid points per side [x y z] : 101 85 93 Total number of grid points : 798405 Generating scoring grids. Percent of protein atoms processed : 0 Percent of protein atoms processed : 10 Percent of protein atoms processed : 20 Percent of protein atoms processed : 30 Percent of protein atoms processed : 40 Percent of protein atoms processed : 50 Percent of protein atoms processed : 60 Percent of protein atoms processed : 70 Percent of protein atoms processed : 80 Percent of protein atoms processed : 90 Percent of protein atoms processed : 100 Writing general grid info to dock_inputs/ece.bmp Writing bump grid to dock_inputs/ece.bmp Writing contact grid to dock_inputs/ece.cnt Writing chemical grids to dock_inputs/ece.chm Writing null chemical grid Writing hydrophobic chemical grid Writing donor chemical grid Writing acceptor chemical grid Writing polar chemical grid Writing energy grids to dock_inputs/ece.nrg Writing attractive VDW energy grid Writing repulsive VDW energy grid Writing electrostatic energy grid Finished calculation. ---------------------------------------------------------------- The Abouve Run produces OUTPUT Files whose size is given below: bezek:~/ng/mm/DockPrep/dock_inputs> ls -l -rw-r--r-- 1 rajkumar csse 798437 Jan 10 11:59 ece.bmp -rw-r--r-- 1 rajkumar csse 15968213 Jan 10 11:59 ece.chm -rw-r--r-- 1 rajkumar csse 1596814 Jan 10 11:59 ece.cnt -rw-r--r-- 1 rajkumar csse 9580876 Jan 10 11:59 ece.nrg bezek:~/ng/mm/DockPrep/dock_inputs> ----------------------------------------------------------------