Molecule Metadata

Molecular modeling software relies on having standard formats for reading molecular structures. One of the most common such formats is the Protein Data Bank (PDB) file. When starting a project, the structure of a molecule is often initially read into CHARMM from a PDB file, which contains information about the component atoms. Atoms are grouped into residues; for example, each amino acid is a residue. Residues are further grouped into chains, or segments, which represent major functional units of the protein. Within the PDB file, the type of each atom, its residue name (RESName) and residue identification number (RESId), and its segment identifier (SEGId) are all specified.

Once a structure is read into CHARMM, the software creates its own internal data structures to represent it. These are discussed in the next subsection.