This is an automated pipeline to fix models that generated by Modeller and use scripts to prepare the ligands and receptors for Smina. Note that the default setting of this pipeline is blind dock, if you want to specify a custom search space,please modify the script docking.sh, also you should change the directory settings of scripts docking.sh, prepare_lig.sh , fix_model.sh.
The pipeline:
(1) fix the model using pdbfixer(fix_model.sh) and use openbabel to add hydrogens and use script prepare_receptor4.py to prepare the receptor. --> (2)prepare the ligands using the script prepare_lig.sh --> (3)start docking using script docking.sh
Openbabel
pdbfixer
SminaYou can obtain these programs from:
http://openbabel.org/wiki/Main_Page
https://github.com/openmm/pdbfixer
https://github.com/mwojcikowski/smina
Your work directory should look like this:
.
├── all.sh
├── docking.sh
├── fix_model.sh
├── ligands
│ ├── ligand1.mol2
|
├── models
│ ├── receptor1.pdb
│ ├── receptor2.pdb
│ ├── receptor3.pdb
│ ├── receptor4.pdb
│ ├── receptor5.pdb
│ ├── receptor6.pdb
│ ├── receptor7.pdb
│ ├── receptor8.pdb
│ ├── receptor9.pdb
│ ├── receptor10.pdb
│ ├── receptor11.pdb
│ ├── receptor12.pdb
│ ├── receptor13.pdb
│ └── receptor14.pdb
├── prepare_ligand4.py
├── prepare_lig.sh
├── prepare_receptor4.pyone command to run this pipeline:
bash all.sh