官方教程链接: http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
步骤 接上文,已经完成了蛋白受体以及配体的准备,加氢加电荷 现在开始准备生成Spheres
生成Sphgen是DOCK的必须
生成Sphgen
rec.ms
#molecular surface file (no default)
R
#sphere outside of surface (R) or inside surface (L) (no default)
X
#specifies subset of surface points to be used (X=all points) (no default)
0.0
#prevents generation of large spheres with close surface contacts (default=0.0)
5.0
#maximum sphere radius in Angstroms (default=5.0)
1.0
#minimum sphere radius in Angstroms (no default)
rec.sph
#clustered spheres file (no default)
终端直接输入sphgen
此时输出文件应为:OUTSPH
文件内容:
density type = X
reading ./rec_dms. dms type R
# of atoms = 1940 # of surf pts = 14469
finding spheres for ./rec_dms.dms
dotlim = 0.000
radmax = 4.000
Minimum radius of acceptable spheres?
1.4000000
output to rec.sph
clustering is complete 49 clusters
选择一个亚类作为bingding site
rec.sph #sphere cluster file
1 #cluster number to process (<0 = all)
N #generate surface as well as pdb file
selected_cluster.pdb #name for output file
此时输出文件为:selected_cluster.pdb
直接使用Chimera打开:
出现的小点即为选择的sphere clusterselected_spheres.sph
1
N
selected_spheres.pdb
输出文件为:selected_spheres.pdb
展示,使用chimera打开selected_spheres.pdb
然后:Actions -> Atoms/Bonds -> sphere
现在看下,spheres将配体完全包围住了