TOP, PRMTOP, PARM7 (AMBER topology)
AMBER specification
Note
The Amber charge is converted to electron charges as used in MDAnalysis and other packages. To get back Amber charges, multiply by 18.2223.
AMBER flag |
MDAnalysis attribute |
ATOM_NAME |
names |
CHARGE |
charges |
ATOMIC_NUMBER |
elements |
MASS |
masses |
BONDS_INC_HYDROGEN BONDS_WITHOUT_HYDROGEN |
bonds |
ANGLES_INC_HYDROGEN ANGLES_WITHOUT_HYDROGEN |
angles |
DIHEDRALS_INC_HYDROGEN DIHEDRALS_WITHOUT_HYDROGEN |
dihedrals / improper |
ATOM_TYPE_INDEX |
type_indices |
AMBER_ATOM_TYPE |
types |
RESIDUE_LABEL |
resnames |
RESIDUE_POINTER |
residues |
Developer notes
The format is defined in PARM parameter/topology file specification. The reader tries to detect if it is a newer (AMBER 12?) file format by looking for the flag “ATOMIC_NUMBER”.