SparcleQC

SparcleQC automates the creation of quantum mechanics/molecular mechanics (QM/MM) input files for electronic structure theory packages, facilitating the study of protein:ligand complexes.

Key Features:

• Multi-package compatibility: Creates QM/MM input files for Psi4, Q-Chem, and NWChem.
• Automated QM subregion preparation: Cuts and caps the QM subregion of the protein.
• Point charge generation: Obtains point charges for the protein environment.
• Boundary charge adjustment: Adjusts charges at the QM/MM boundary.
• PDB input support: Accepts protein:ligand complexes in Protein Data Bank (PDB) file format.
• Python API: Provides a Python API for programmatic access to functionality.

Scientific Applications:

• Protein:ligand interaction studies: Enables automated preparation of input files for QM/MM calculations of protein:ligand complexes.
• Interaction energy calculations: Supports QM/MM calculations that return accurate interaction energies in minutes compared to days for fully quantum mechanical computations.

Methodology:

SparcleQC takes a protein:ligand complex in PDB format and generates QM/MM-like input files containing quantum mechanical representations of the ligand and a small section of the protein, surrounded by point charges representing the rest of the protein.