How can we introduce new Atom Types in the parameters file of AutoDock Vina?

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Sargol Mazraedoost

Introducing new atom types in the parameters file of AutoDock Vina involves modifying the force field parameters to accommodate the specific atom types you want to include. AutoDock Vina typically uses a force field based on AMBER (Assisted Model Building with Energy Refinement), so you would need to modify the AMBER parameter files. Here are the general steps to introduce new atom types in AutoDock Vina:

Understand AMBER Parameters: Familiarize yourself with the AMBER force field parameters and file formats. AMBER uses parameter files like frcmod and prmtop to define force field parameters for atoms and molecules.

Create or Modify Parameter Files: You will need to create or modify the appropriate AMBER parameter files to include the new atom types. This includes the atom types, charges, van der Waals parameters (Lennard-Jones parameters), and other relevant parameters.

Define Atom Types: In your parameter files, define the new atom types you want to introduce. You will need to specify the atom name, charge, and parameters related to its interactions with other atoms (e.g., van der Waals radius and well depth).

Maintain Compatibility: Ensure that the new atom types are compatible with the existing force field parameters in terms of units and parameter naming conventions.

Test and Validate: Before using the modified parameter files in molecular docking simulations with AutoDock Vina, it's essential to validate the parameters by running test simulations. You can use molecular dynamics simulations or other software tools to ensure that the new atom types behave as expected.

Update AutoDock Vina Configuration: Modify the AutoDock Vina configuration files to reference your custom AMBER parameter files with the new atom types. Ensure that the configuration files correctly specify the force field parameters, including atom types and charges.

Perform Docking Simulations: Run molecular docking simulations using AutoDock Vina with the updated configuration files and custom AMBER parameter files. These simulations will use the new atom types you introduced.

Analyze Results: Analyze the results of your docking simulations to evaluate the interactions of the new atom types with the receptor and ligands. Check for any anomalies or unexpected behavior.

Iterate and Refine: Based on the results and feedback from your simulations, you may need to iterate and refine the parameters for the new atom types to improve their accuracy and reliability in simulations.

Jobin Thomas

You can add this line in the AD4 parameters.dat file

atom_par Ru 2.96 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding

Regards

Vaishnu S.K.

Hi Sargol Mazraedoost ,

I appreciate your answer. Can you please elaborate the "updating the vina configuration' part. I have tried to do so, but the error persists.