ChargeCalculator:Terminology

Structural elements

Any input file containing molecular structures is parsed and interpreted at several levels.

Molecule

In the ACC environment, a molecule represents the sum of all structural elements in the input file, regardless of other annotations within the file (e.g., ATOM vs HETATM records, chain identifiers marking different components of a complex, etc.). In other words, molecule is used here as an umbrella term for everything from simple compounds to biomacromolecular complexes made up of proteins, nucleic acids, ligands, ions, water, etc. ACC thus assigns a unique identifier (molecule ID) to each molecule according to the input file name.

Atom

Each molecule is made up of a set of atoms. In the ACC environment, each atom is uniquely identified in the input file by its chemical element and atom serial number. Additional useful information can be used in the characterization of each atom, if such information is available in the input file (atom name and residue details).

Residue

We generally use the term residue to refer to any component of a biomacromolecule. Within the ACC environment, any collection of atoms bound by chemical bonds (covalent, coordinative or ionic) is considered a residue if this fact is appropriately indicated in the input file. Specifically, all the atoms that make up a residue should have the same residue name (3-letter code) and residue serial number. Not all file formats include residue information, but this has no bearing over the charge calculation procedure in ACC.

Charges

ACC operates with charges at several resolutions.

Atomic charge

The smallest resolution visible in ACC is at the atom level. We use the term atomic charge to refer to a single value which represents the algebraic sum between the atom's nuclear charge (given by the number of protons in the nucleus), and the amount of molecular electron density associated to this atom. In space, the atomic charge is given at the position of the atomic nucleus.

Residue charge

The next level of resolution in ACC refers to residues. We use the term residue charge to refer to the sum of atomic charges for all atoms which belong to one residue. The origin of each atom is established according to residue name and serial number, provided this information is present in the input file.

Molecular charge

The total molecular charge is a formal value based on the molecular structure and the protonation state of all ionizable groups. The process of atomic charge calculation in ACC consists of distributing the amount of electron density given by the total molecular charge across the molecule, to each atom based on certain criteria and algorithms. Thus, the sum of atomic charges for all atoms in a molecule equals the molecular charge. Similarly, the sum of residue charges for all residues in a molecule equals the molecular charge.

Work flow

EEM parameters

The Electronegativity Equalization Method (EEM) is the procedure by which atomic charges are calculated. EEM employs special parameters for each type of atom. An EEM parameter set generally covers H,C,N,O, but also halogens, metals, etc, depending on what type of molecules were targetted during the development of the parameters. Many EEM parameter sets have been published in literature, and are available here as built-in parameter sets. 'ChargeCalculator' will try to recommend a set suitable for the molecules you uploaded. Click 'More' and 'Show sets' for the full list. Select one or more parameter sets for your computation. You may also add your own set of parameters by clicking 'Add'. It's often useful to just modify one of the existent sets, for example if parameters for only one atom are missing, you may try to derive them and just include them in the established parameter set. To do this, click on the set of interest in the list, and then 'View XML' on the panel to the right. Copy/paste the content into the 'Add' window, make your modifications, and save this parameter set under a unique name.

Computation parameters

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