生成 Grid
围绕活性位点创建一个box 使用指令：showbox < box.in box.in的文件格式为：
输出文件：rec_box.pdb Chimera可直接打开
生成grid 使用指令为：grid -i grid.in -o grid.out grid.in格式为：
输出为：grid.out,grid.bmp,grid.nrg 计算需要花费时间 输出后查看grid.out文件
代码语言：javascript复制
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
__________________Job_Information_________________
launch_time Sat Apr 18 16:26:39 2020
host_name unknown
memory_limit -1
working_directory /Users/sujiaqi/Desktop/PyDrug.0.4/PyDrug_going/PyDrug_DOCK/structure_prepara
user_name sujiaqi
________________General_Parameters________________
compute_grids yes
grid_spacing 0.3
output_molecule no
________________Scoring_Parameters________________
contact_score no
energy_score yes
energy_cutoff_distance 9999
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 rec-1htp-dock-prep.mol2
box_file rec_box.pdb
vdw_definition_file /Users/sujiaqi/Program/dock6/parameters/vdw_AMBER_parm99.defn
____________________File_Output___________________
score_grid_prefix grid
Reading in coordinates of receptor.
CHARGED RESIDUE SER : 1.000
CHARGED RESIDUE ASP : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE HIS : 1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE HIS : 1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE ASP : -1.000
CHARGED RESIDUE HIS : 1.000
CHARGED RESIDUE ASP : -1.000
CHARGED RESIDUE HIS : 1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE ASP : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE ASP : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE ASP : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE LYS : 1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE GLU : -1.000
CHARGED RESIDUE ASP : -1.000
Total charge on rec-1htp.pdb : -7.000
Reading in grid box information.
Box center of mass : -6.701 22.781 2.973
Box dimensions : 27.562 35.543 32.116
Number of grid points per side [x y z] : 93 120 109
Total number of grid points : 1216440
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
Writing general grid info to grid.bmp
Writing bump grid to grid.bmp
Writing energy grids to grid.nrg
Writing attractive VDW energy grid
Writing repulsive VDW energy grid
Writing electrostatic energy grid
Finished calculation.
