Instructions to use Mini Docking

Requirements:

Install Dock6, MGL Tools, Chimera and Autodock Vina. 
In next release we will provide a automatized installation of this programs.

Running the Mini Docking:

1

Run the configure.sh in terminal and type the place when Dock6 is installed:
./configure.sh

As example, if the Dock6 was installed in /opt/dock6 type /opt.

2

The file MDtimer.py has a timer on line 55, which is the timeout of a is at 5400 seconds, but it can be much less, for example can be used 3600.


3

To start all crystallographic scripts and pdbs they must be in the same folder inside this folder; there must be a folder in format ligandsXXXX, where XXXX must be replaced by the target code where these ligands will be anchored this serves to make more than one VS at a time.
As a example the molecule 6W79 is presented with the target as 6W79.pdb and ligands in folder ligands6W79.

4

To start the execution run script MDstart.py with the following command:
python3 MDstart.py

5

The program will ask as input the codes of the crystallographic ligands of each target to separate the complex. Also, the program will ask to create a database to help future executions.