The MMTSB Tool Set contains a variety of tools for general-purpose all-atom protein modeling that are described in this section. They are intended as support utilities for structure prediction and refinement applications, but since they are equally useful for other protein modeling purposes they are described here separately from the other more specific tools for structure refinement, evaluation, and prediction.

"All-atom" means that the protein is represented in atomic detail as opposed to low-resolution models with one or few pseudo-particles per amino acid residue. United-atom models without explicit non-polar hydrogen atoms (e.g. the CHARMM19 force field) are also considered "all-atom" since they represent all other atoms in atomic detail. All-atom protein models are expected in PDB format. Other formats such as mmCIF are not supported at this point.

The force-field based all-atom protein modeling relies primarily on CHARMM. The Amber program suite is also supported although to a more limited extent. The default force fields are CHARMM19 (only polar hydrogens) and CHARMM22 (all hydrogen atoms). Other protein force fields (MMFF, Amber, OPLS e.g.) may be used alternatively as long as CHARMM topology and parameter files are available.

The all-atom modeling tools can handle single- or multi-chain proteins with canonical residue and atom names. They are designed in particular for regular proteins and peptides but other chemical components such as solvent molecules, ions, ligands, or nucleic acids may be included if additional parameter and topology information is provided for CHARMM.

The Tool Set components for general-purpose all-atom modeling are divided into three classes:

• PDB file manipulation
• Protein structure completion and subselection
• Force-field based functions
  (energy evaluation, minimization, molecular dynamics)