Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing

2012 December 21; 52(12): 3144–3154 | K. Vanommeslaeghe and A. D. MacKerell Jr
The article presents the algorithms for bond perception and atom typing in the CHARMM General Force Field (CGenFF), a force field designed for computer-aided drug design. The CGenFF atom typer assigns atom types to molecules by first associating attributes such as valence, bond order, and ring membership. These attributes are then used to assign CGenFF atom types through a programmable decision tree, allowing for straightforward implementation and updating of complex atom typing rules. The atom typer was validated on 477 model compounds and 126 test molecules, demonstrating its accuracy and flexibility. The program is available online at <https://www.paramchem.org/>. Molecular mechanics force fields are widely used in computer-aided drug design to study drug-like molecules and their interactions with biological systems. The CGenFF force field extends the CHARMM additive biomolecular force field to drug-like molecules, enabling accurate simulations of drug-like molecules and their interactions with biological systems. The atom typing process involves identifying and categorizing rings in the molecule, resolving aromatic bonds into a single resonance structure, and assigning atom types based on a programmable decision tree. The CGenFF atom typer is designed to handle complex chemical environments and provides a flexible tool for computer-aided drug design projects.The article presents the algorithms for bond perception and atom typing in the CHARMM General Force Field (CGenFF), a force field designed for computer-aided drug design. The CGenFF atom typer assigns atom types to molecules by first associating attributes such as valence, bond order, and ring membership. These attributes are then used to assign CGenFF atom types through a programmable decision tree, allowing for straightforward implementation and updating of complex atom typing rules. The atom typer was validated on 477 model compounds and 126 test molecules, demonstrating its accuracy and flexibility. The program is available online at <https://www.paramchem.org/>. Molecular mechanics force fields are widely used in computer-aided drug design to study drug-like molecules and their interactions with biological systems. The CGenFF force field extends the CHARMM additive biomolecular force field to drug-like molecules, enabling accurate simulations of drug-like molecules and their interactions with biological systems. The atom typing process involves identifying and categorizing rings in the molecule, resolving aromatic bonds into a single resonance structure, and assigning atom types based on a programmable decision tree. The CGenFF atom typer is designed to handle complex chemical environments and provides a flexible tool for computer-aided drug design projects.
Reach us at info@study.space
[slides and audio] Automation of the CHARMM General Force Field (CGenFF) I%3A Bond Perception and Atom Typing