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# 4.1. Topology readers — `MDAnalysis.topology`

This submodule contains the topology readers. A topology file supplies the list of atoms in the system, their connectivity and possibly additional information such as B-factors, partial charges, etc. The details depend on the file format and not every topology file provides all (or even any) additional data. As a minimum, a topology file has to contain the names of atoms in the order of the coordinate file and their residue names and numbers.

The following table lists the currently supported topology formats.

Table of Supported topology formats
Name | extension | remarks
--- | --- | ---
CHARMM/XPLOR | psf | reads either format, but only atoms and bonds information is used at the moment; `MDAnalysis.topology.PSFParser`
CHARMM* | crd | “CARD” coordinate output from CHARMM; deals with either standard or EXTended format; `MDAnalysis.topology.CRDParser`
Brookhaven* | pdb | a simplified PDB format (as used in MD simulations) is read by default; the full format can be read by supplying the permissive=False flag to `MDAnalysis.Universe`; `MDAnalysis.topology.PrimitivePDBParser` and `MDAnalysis.topology.PDBParser`
PQR* | pqr | PDB-like but whitespace-separated files with charge and radius information; `MDAnalysis.topology.PQRParser`
PDBQT* | pdbqt | file format used by AutoDock with atom types t and partial charges q. Module: `MDAnalysis.topology.PQBQTParser`
GROMOS96* | gro | GROMOS96 coordinate file; `MDAnalysis.topology.GROParser`
Amber | top prmtop | simple Amber format read (only supports a subset of flags); `MDAnalysis.topology.TOPParser`

Formats marked with ans asterisk * also hold coordinates and thus can be used as the sole argument to `MDAnalysis.Universe` to set up a system.

See also

Coordinates modules with the Table of Supported coordinate formats

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