Small-molecule reactions

pdb2reaction also analyzes reaction paths of small molecules, not only enzyme cluster models. Give the reactant (R) and product (P) as XYZ/GJF/PDB/CIF structures and run all without -c; with no -c, the cluster-model extraction is skipped and the input structures are analyzed as they are.

First example

examples/aromatic_claisen/ holds the reactant and product of an aromatic Claisen rearrangement (allyl phenyl ether → 6-allylcyclohexa-2,4-dien-1-one); run the command below in examples/.

pdb2reaction all -i aromatic_claisen/reactant.xyz aromatic_claisen/product.xyz -q 0 --tsopt --thermo

The run searches the minimum energy path (MEP) and continues to transition-state (TS) optimization, the intrinsic reaction coordinate (IRC), and vibrational analysis with thermochemistry. Scientific status: success under ====== Pipeline summary ====== near the end of the terminal output means success; scientific_status in summary.json has the same value.

Input notes

  • Formats: XYZ, GJF, PDB, and CIF are accepted. Several structures must have the same atoms in the same order.

  • Charge and spin: set the charge with -q and the spin multiplicity with -m (default 1).

  • Other input modes: the Scan-list mode, which builds the path from one structure by a scan, and the TS-only mode, which starts from a TS candidate, also work without -c.

  • Reactions in solution: --solvent adds the xTB solvation correction (xTB solvent correction).

See also