acpype.mol.Atom

class acpype.mol.Atom(atomName: str, atomType: AtomType, id_: int, resid: int, mass: float, charge: float, coord: List[float])

Bases: object

Atom Object Definition

Charges in prmtop file are divided by 18.2223 to be converted in units of the electron charge.

To convert ACOEF and BCOEF to r0 (Å) and epsilon (ε: kcal/mol), as seen in gaff.dat for example, for a same atom type (i = j):

\[\begin{split}r_0 &= 1/2 * (2 * A_{coef}/B_{coef})^{1/6} \\ \epsilon &= 1/(4 * A_{coef}) * B_{coef}^2\end{split}\]

To convert r0 and epsilon to ACOEF and BCOEF:

\[\begin{split}A_{coef} &= \sqrt{\epsilon_i * \epsilon_j} * (r_{0i} + r_{0j})^{12} \\ B_{coef} &= 2 * \sqrt{\epsilon_i * \epsilon_j} * (r_{0i} + r_{0j})^6 \\ &= 2 * A_{coef}/(r_{0i} + r_{0j})^6\end{split}\]

where index i and j for atom types. Coordinates are given in Å and masses in Atomic Mass Unit.

Returns:

atom object

Return type:

acpype.mol.Atom

__init__(atomName: str, atomType: AtomType, id_: int, resid: int, mass: float, charge: float, coord: List[float])
Parameters:

  • atomName (str) – atom name

  • atomType (AtomType) – atomType object

  • id (int) – atom number index

  • resid (int) – residues number index

  • mass (float) – atom mass

  • charge (float) – atom charge

  • coord (List[float]) – atom (x,y,z) coordinates

Methods

__init__(atomName, atomType, id_, resid, ...)

param atomName:

atom name