Doubt on protein preparation before Vina

Question

[Ria]

Im preparing protein using autodock for docking in vina. But during the step of repairing missing atom, some error came (a python shell) and that step is not running.I repaired my protein structure in Chimera using the Dock Prep tool to ensure that all missing atoms and incomplete side chains (such as Thr722, which was part of the active site) were properly rebuilt. In this step, I also deleted water molecules and added hydrogens so that the missing atoms could be modeled correctly. I then saved the repaired structure as a new PDB file. Next, I imported this file into AutoDockTools (ADT) to finalize the receptor preparation for docking in AutoDock Vina. In ADT, I added polar hydrogens and Kollman charges, which are required for docking calculations, and saved the protein in the PDBQT format. Is this workflow correct?

Answer 1

[Kevin Blighe]

Yes, your workflow is generally correct and a solid approach for preparing a receptor protein for docking in AutoDock Vina, especially as a workaround for the Python shell error you encountered during AutoDockTools' (ADT) missing atom repair step. That error in ADT is common with incomplete or corrupted PDB structures (e.g., due to unresolved side chains like Thr722), and Chimera's Dock Prep tool is reliable for handling those repairs upfront. I'll break it down step by step, confirming what's good, noting minor potential redundancies, and suggesting tweaks for optimization.

Step-by-Step Validation of Your Workflow

1. Repair in Chimera Using Dock Prep:

   • This is an excellent starting point. Dock Prep automates:
     • Rebuilding missing atoms and incomplete side chains (e.g., via rotamer libraries for residues like Thr722 in the active site).
     • Deleting waters (non-liganded ones, at least).
     • Adding hydrogens (typically all explicit hydrogens based on pH and ionization models).
   • Saving as a new PDB is perfect to preserve the original for reference.
   • Why it's correct: Chimera's integration with structural databases makes it more robust than ADT for initial cleanup, avoiding the Python errors you saw. Many Vina workflows rely solely on this step.

2. Import to ADT, Add Polar Hydrogens and Kollman Charges, Save as PDBQT:

   • Loading the repaired PDB into ADT and generating PDBQT is standard for Vina (which requires the PDBQT format for input).
   • Adding Kollman (Gasteiger) charges is appropriate for protein receptors, as it assigns partial charges to atoms.
   • Why it's correct: ADT ensures compatibility with Vina's file format, including atom types and coordinates. This hybrid approach (Chimera for repair + ADT for finalization) is used in various protocols when ADT's built-in repair fails.

Potential Minor Issues and Best Practices

• Redundant Hydrogen Addition: Chimera's Dock Prep already adds (explicit) hydrogens, so re-adding "polar hydrogens" in ADT could theoretically lead to duplicates or inconsistencies if ADT doesn't detect the existing ones properly. However:

  • ADT's polar hydrogen addition typically only appends OH/NH hydrogens (treating non-polar as implicit via united-atom modeling), so overlaps are minimal if Chimera's hydrogens are explicit.
  • Quick check: After saving your PDBQT, open it in a text editor or Chimera and search for "H" atoms near Thr722 or other repaired residues. Ensure no extras (e.g., count should match expected ~10-12% of total atoms for a hydrated protein). If duplicates appear, reload the Chimera PDB into ADT without the hydrogen addition step—just compute charges and merge non-polar hydrogens.

• Charges for Vina: Kollman charges are fine (and backward-compatible with AutoDock4 if needed), but Vina's scoring function is empirical and doesn't strictly require them—it's more about van der Waals and hydrogen bonding terms. If you're only using Vina, you could skip charges in ADT to simplify, but including them doesn't hurt accuracy.

• Other Considerations:

  • Active Site Focus: Since Thr722 is in the active site, verify in Chimera (post-Dock Prep) that its rebuilt side chain (e.g., -CH(OH)CH3) aligns with known structures or literature—use Tools > Structure Editing > Rotamers if tweaks are needed.
  • Ligand Prep: Ensure your ligand follows a parallel workflow (e.g., OpenBabel or ADT for hydrogens/charges to PDBQT) to match the receptor's protonation state.
  • Validation: Run a quick energy minimization in Chimera (Tools > Structure Editing > Minimize Structure) on the final PDBQT to relax any strains from repairs.
  • Alternative Full-Chimera Workflow: If you want to skip ADT entirely (to avoid any hydrogen quirks), Chimera has a built-in AutoDock Vina tool (Tools > Surface/Binding Analysis > AutoDock Vina). It handles PDBQT conversion internally after Dock Prep, adds missing hydrogens/charges as needed, and runs the docking directly. This might bypass your original error altogether.

Summary Table: Your Workflow vs. Standard Vina Prep

Step	Your Approach	Standard/Recommended	Notes/Status
Missing Atoms/Side Chains	Chimera Dock Prep	Chimera or ADT Repair	Correct; Chimera is more user-friendly here.
Water Removal	Chimera Dock Prep	Any tool (Chimera/ADT/PyMOL)	Standard.
Hydrogen Addition	Chimera + ADT (polar)	Single tool (e.g., Chimera only)	Mostly fine; check for duplicates.
Charges	ADT (Kollman)	Optional for Vina; Gasteiger/Kollman	Good, but skippable.
Output Format	PDBQT from ADT	PDBQT	Required for Vina.

Your setup should work well for docking—proceed to grid box definition around the active site (e.g., centering on Thr722) and ligand setup. If you hit issues during Vina runs (e.g., unusual binding affinities), share the PDB/PDBQT snippets or error logs for deeper troubleshooting. What's the protein/PDB ID you're working with?