Workspace not created
Start a new workspace before uploading receptors or ligands. The browser workflow creates a workspace automatically on page load.
Common setup checks before rebuilding a docking package.
Most docking-preparation errors come from missing inputs, incomplete centers, unsupported file formats, external conversion tools, or package-mode settings. Use these checks before repeating a long workflow.
How to debug failed docking package preparation
Troubleshooting should start with the earliest missing workflow state: workspace creation, receptor registration, saved docking center, receptor preparation log, ligand upload state, package mode, and generated artifacts. This narrows failures before users repeat long upload or conversion steps.
Decision path
Check the earliest missing state before repeating later steps.
A failed package build is often the final symptom, not the first problem. Work backwards through the workflow: workspace, receptor registration, center table, receptor preparation log, ligand upload state, package mode, and generated artifact list.
This keeps debugging narrow and avoids re-uploading large files when the real issue is a missing center or a deployment dependency such as Open Babel.
Receptor is not centered
Open the receptor in the viewer and save a center using ligand, residue, XYZ, or clicked-atom selection before running preparation.
PDBQT conversion failed
Check whether the deployment has the required conversion executable available, such as Open Babel, and inspect the preparation log.
CSV ligand build fails
CSV ligand uploads require a SMILES column selection before package generation. Confirm the selected column contains valid SMILES strings.
Build ZIP button disabled
The package step stays disabled until receptors are centered/prepared and ligand inputs have been uploaded.
LSF mode is unavailable
Scheduler-oriented package generation depends on deployment configuration. Public deployments may default to portable ZIP mode.
Confirm state exists
Reload the page or API state and confirm the workspace still contains receptors, centers, ligand status, and any generated artifacts you expect.
Read the first failing log
If receptor conversion fails, inspect the preparation log before changing ligand files or package mode. Conversion failures usually happen earlier in the pipeline.
Verify package assumptions
Portable packages and scheduler-oriented packages have different expectations. Confirm which mode is enabled for the deployment and which downstream environment will run Vina.
Still stuck?
Include the workflow step, input type, package mode, and concise error text when reporting an issue.
FAQ
Troubleshooting FAQ
Why is my build button unavailable?
The build step depends on a valid workspace, centered and prepared receptors, uploaded ligand inputs, and any required CSV configuration. Check those states before attempting package generation.
What should I check when PDBQT conversion fails?
Inspect the prep log, confirm the receptor input is parseable, review cleanup choices, and verify that the deployment has the required conversion executable such as Open Babel.
What information helps with a bug report?
Include the workflow step, browser or API path, input type, package mode, concise error text, and whether the issue is reproducible with non-confidential example files.