Troubleshooting

Download failures for CCD definitions

If downloadTemplate() returns False, verify internet connectivity and that the residue name exists in the PDB Chemical Component Dictionary. Proxy settings must be configured via your environment or system network settings.

No atoms found

PDBFixer raises an exception if the loaded structure has zero atoms. Confirm the input file path or URL and that you are passing the correct source argument.

Missing templates for nonstandard residues

If findNonstandardResidues() suggests replacements that lack templates, register your own via registerTemplate() or allow downloads with downloadTemplate().

Slow solvation

addSolvent() can be compute-intensive for large systems. Consider running with an explicit openmm.Platform tuned for your hardware or increasing padding only as needed.

Reporting issues

If you encounter problems, please file an issue or open a pull request with reproduction steps. Include the input structure and the sequence of PDBFixer calls you executed.