1. You can either use a multi-mol2 or mol/sdf file containing 3D structures of many ligands.
2. Split your mol2 into several singleton mol2 files.
3. Use the following shell scripts to automate the docking runs. The scripts are available in the Download section .
How to use these scripts:
list.txt
- this file contains the list of the ligands to be used, single name per line.
template.txt
- this is the general keyword file which contains all the docking settings. You need to modify with the proper Protein name, BindingSite and IS files.
script.sh
- this is the script itself. The command to use is the following:
prompt$ sh script.sh &
You need to execute this script in the fitted folder. The script will create automatically the required keyword file in the keyword folder and execute fitted for all the ligands listed in the list.txt file.
