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4.5. AMBER PRMTOP topology parser

Reads a AMBER top file to build the system. It uses atom types, partial charges and masses from the PRMTOP file.

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”.

The parser raises a TOPParserError if it fails to read the topology file.

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.

Changed in version 0.7.6: parses both amber10 and amber12 formats

exception MDAnalysis.topology.TOPParser.TOPParseError[source]

Signifies an error during parsing of a Amber PRMTOP file.

x.__init__(...) initializes x; see help(type(x)) for signature

MDAnalysis.topology.TOPParser.parse(filename)[source]

Parse Amber PRMTOP topology file filename.

Returns:MDAnalysis internal structure dict.