- Docking Simulation 137
For Microsoft Windows users, installing MSYS system (from http://
http://www.mingw.org/wiki/msys),,) Cygwin (https://www.cygwin.com/), or simi-
lar systems are recommended.
The approach described here is different from the one in the official
site. If you prefer the official one, please navigate to http://vina.scripps.
edu/tutorial.html or search ‘vina video tutorial’ in your search engine.
Materials
- Ligand structure file which contains only one compound inside.
- Protein target structure file.
- OpenBabel^13 installation.
- Autodock Vina application which can be downloaded from http://vina.
scripps.edu/download.html.
Procedure
I. Navigate into an appropriate directory (e.g., where your ligand and
protein structure files are stored, or where you want to store your
result) in the text-based shell of your choice.
In Windows, use command prompt; in GNU/Linux, use of any virtual
terminal application will do.
II. Use the following command to prepare ligand in your shell prompt:
cat ligand.sdf |obabel -isdf --AddPolarH -opdbqt >
ligand.pdbqt
or
obabel -isdfligand.sdf --AddPolarH -opdbqt Oligand.pdbqt
If you are using ligand in mol2 format, change underlined part to mol2;
if you are using ligands in pdb format, change underlined part to pdb.
If the coordinates of the ligand is in 2D, please add--gen3Dswitch,
like this:
cat ligand.sdf | obabel -isdf --AddPolarH --gen3D-opdbqt
> ligand.pdbqt
or
obabel -isdf ligand.sdf --AddPolarH --gen3D -opdbqt
-Oligand.pdbqt