Atom typing behavior

To use a classical forcefield each atom should be given a type, and a partial charge. The power of the UFF forcefield is that this goes automatically. For other forcefields this has to be done by hand, possibly with the help of an external program. Furthermore, such forcefields typically cover only a fraction of all chemical elements.

UFF

Atom typing is the process of matching MM atom types to elements. For example, a Carbon atom becomes a C_1, C_2, C_3 or C_R, depending on the number (and type) of bonds it has to neighboring atoms. UFF is capable of finding a matching MM atom type on its own, but might not always succeed in doing so. When doing calculations with UFF, it is important to check the beginning of the output file, as the program will print the detected MM atom types there. You can also take matters into your own hands, and tell UFF what MM atom types you want it to use (see the section on Input and examples).

The atom typing in UFF is mostly controlled by the elements and mmatomtypes parameter files, however, some part of it is hidden in the code itself and is (at the moment) not accessible to users. This is done by UFF to differentiate between:

  • Carbon: double-bonded sp2 carbon (C_2) vs aromatic carbon (C_R), if any of the orders are close to 2, it’s C_2.
  • Oxygen: having a bond to silicon gives O_3_z; otherwise, having bond order of 1.44 or higher gives O_R, provided that the partner is not a hydrogen. Otherwise, it’s just an O_3.
  • Sulfur: having a bond order greater than 1.3 gives aromatic S_R.

By default, zero charges are used, unless a water molecule is detected.

Other forcefields

See also

Antechamber integration for GAFF forcefields

The specification of these forcefields is in forcefield files. The two supported formats are now “.ff” (originating from the ADF and QUILD programs) and the much more widely used amber “.dat” files.

However, using the GUI and pdb files might be helpful to get atom types. You can load a pdb file in amsinput and then under the regions you will find the residues. Still, charges need to be set by hand.