AutoDock Note
Docking is one of the key problem bringing the substrate to the enzyme modeling. But most current docking methods performs poorly with larger substrates. This note record usages of the AutoDock Vina for testing.
Site Specific Docking (Autodock Vina)
就是通过grid box的选取来决定site
Input files
1. pdbqt file for protein
Start with the pdb file of the apo protein:
Remove water (Can it work with the key water?)
Add Hydrogens (What’s the difference between polar only or not)
File formating: (pdb) -> (pdbqt)
2. pdbqt file for ligand
File formating: (pdb) -> (pdbqt)
3. Configuration file
Grid bot setting
This limited grid box achieves the site specification by containing only the key residues.
所以需要自动决定Grid box来实现高通量 调查一下一般的选择条件
A txt file that contains (grid.txt)protein
spacing ###
npts ## ## ##
center ## ## ##Job setting (conf.txt)
receptor= protein.pdbqt
ligand= SO.pdbqt
center_x= ###
center_y= ###
center_z= ###
size_x= ##
size_y= ##
size_z= ##
out= vina_outSO.pdbqt
log= logSO.txt
exhaustiveness= 8
Run Vina
./vina -–config conf.txt -–log logSO.txt |