CAN

CAN automates updating charge, atom type, and atom name attributes in mol2 molecular coordinate files to prepare inputs for molecular dynamics (MD) simulations.

Key Features:

• Automation of Molecular File Preparation: Processes mol2 files and updates charge, atom type, and atom naming using a library of amino acid monomers as templates.
• Versatility Across Molecular Sizes: Applies to molecular systems ranging from small molecules to large protein complexes.
• Handling of Diverse Amino Acid Residues: Supports both native and non-native amino acid residues for modified proteins and peptides.

Scientific Applications:

• Molecular Dynamics Simulations: Prepares coordinate files for MD simulations, including compatibility with AmberTools workflows.
• Protein Structure Analysis: Produces structural files for polypeptides to support studies of protein folding, stability, and interactions.
• Drug Design and Discovery: Enables modeling and simulation of candidate drug molecules and their interactions with target proteins.

Methodology:

Processes mol2 molecular structure files and, using a predefined library of amino acid monomers as templates, systematically updates charge, atom type, and atom name attributes.