VINA UI

A desktop UI for AutoDock Vina

This UI was developed to make running AutoDock Vina a seamless process for anyone wishing to simulate receptor/ ligand binding

Notes:

• This Application requires AutoDock Vina installed on the device. To install AutoDock Vina, see Installing Vina
• An executable/ script is provided to eliminate the need for the terminal
  • This application can still be run via an IDE or terminal by running main.py

Running VinaUI for the First Time

Initializing your Paths

• A dialog window will appear prompting you to initialize your paths
• {Image of Initialize Path Dialog Goes Here}

1. Designate the location of vina
   • Windows: C:\Program Files (x86)\The Scripps Research Institute\Vina\Vina.exe
   • Mac/ Linux:
2. Designate a directory/ folder for your data to be accessed/ stored
   • You may designate where each component of your data goes with the "Sub Paths" option
   • Notes:
     • The configuration file will be created and stored in the parent Data directory
     • You must specify your data directory before continuing/ changing your Sub Paths
3. Once you have designated your paths, click "Ok"

• Note: You will have the option to change any directory you wish later (Config Menu -> Reconfigure Paths)

Go to where your designated your data directories and add in your receptors and ligands

❗ Make sure each receptor and ligand is in a *.pdbqt format

Setting up your Configuration File

Here your will designate the parameters for vina to run

• {Image of Main VinaUI Window Goes Here}

1. Select a receptor
2. Select a ligand (if you are running only one)
3. Fill in the GridBox parameters: Center X,Y,Z ; Size X,Y,Z ; Exhaustiveness
4. Fill in a seed or check the "random seed"
   • Note: If "Random Seed" is selected, each ligand run on vina will use a randomized seed (Including when running All ligands)
5. Determine if you would like to run the "Selected Ligand" or "Run All Ligands" within a desired ligand directory (Click respective button)

If "Run Selected Ligand" was chosen then vina will run with the given GridBox, Exhaustiveness, and Seed parameters

If "Run All Ligands" was chosen a new dialog will appear

Running All Ligands

• A dialog window will appear with the option to change your ligand directory (for this run only)
• {Image of Run All Ligands Dialog Goes Here}
• You are given the option to sort the output by binding affinity
  • If you choose to sort, you must designate a directory for the output files to go
    • Once you begin the run, a new directory will be made with the name "RUN_All_Ligands..." followed by the date and time
    • Once the run is complete a "SORTED_LIST" follow by the date and time will be created and the file will contain all ligands ran along with their respective binding affinities (In order of best to worst binding)
  • If sort is not selected, then all ligand output and log files will be placed in their previously initialized directories
• Click "Ok" to run all the ligands with the configuration data you specified on the previous window
  • Note: If you selected "Randomized Seed" each ligand will be run with a different randomized seed