3.1 Partial Charges and Atomic Radii

There are three essential quantities for any PB calculation: coordinates, dielectric model (including radii), and charge. Coordinates will come from the atomic coordinates of the input molecule, but partial charges and the dielectric model deserve some extra attention.

Charges and radii can be calculated at run-time using functions provided by OEChem or other OpenEye toolkits (AM1-BCC charges from QuacPac for example). The dielectric model consists of both the value of the inner and outer dielectric, as well as how the dielectric adjusts from one to the other. ZAP uses atomic radii as the basis for its dielectric algorithm. By default, we recommend using Bondi VdW radii which can be set on a molecule using the function OEAssignBondiVdWRadii Or you can set specific radii on an atom-by-atom basis using the OEAtomBase::SetRadius function.

The current recommended value for the inner and outer dielectrics for a molecule in an aqueous solution are 1.0 and 80.0. Therefore, these are the default values for the OEZap and OEBind implementations. The historic value for the inner dielectric is 2.0, and this value may be set using the SetInnerDielectric method. Additionally, the default value for the inner dielectric of the OEET implementation remains at 2.0 for the time being.

Accurate PB calculations also depend on quality atomic charges. In OEChem, we provide MMFF94 partial charges as the lowest level of charges that we consider usable in PB. The examples that follow will use these charges, so that they don't depend on any toolkits beside ZAP and OEChem. But for production use, we recommend AM1-BCC charges

If your input file format can store partial charges and/or radii, you can use those values instead of calculating them at run time. OEB files can store radii and partial charges, so they serve as a useful intermediate file between many OpenEye programs. Note that charges and radii will only be written to an OEB file if they are present on the molecule when written.

Atomic charges can come in a PDB file, along with atomic radii, in the form of the extra fields added after the coordinates. This style originated with DelPhi. Note that to get OEChem to read charges and radii from these fields in a PDB file, you need to set a specific flavor on the input oemolistream before reading any molecules from the stream.

if (ifs.GetFormat()==OEFormat::PDB)
  ifs.SetFlavor(OEFormat::PDB,OEIFlavor::PDB::Default|OEIFlavor::PDB::DELPHI);

Listing:3.1

Charges can also come from a MOL2 file that has entries in the charge field, but radii will still need to be assigned using a function like OEAssignBondiVdWRadii

				ZAP Electrostatics at OpenEye C++ Programming Manual

				ZAP Electrostatics at OpenEye C++ Programming Manual