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# 4. Topology modules

The topology module contains the functions to read topology files. MDAnalysis uses topology files to identify atoms and bonds between the atoms. It can use topology files from MD packages such as CHARMM’s and NAMD’s PSF format or Amber’s PRMTOP files. In addition, it can also glean atom information from single frame coordinate files such the PDB, CRD, or PQR formats.

Typically, MDAnalysis recognizes formats by the file extension and hence most users probably do not need to concern themselves with classes and functions described here. However, if MDAnalysis does not properly recognize a file format then a user can explicitly set the topology file format in the topology_format keyword argument to `Universe`.

Contents

- 4.1. Topology readers — `MDAnalysis.topology`
- 4.2. Common functions for topology building — `MDAnalysis.topology.core`
- 4.3. MDAnalysis topology tables
- 4.4. PSF topology parser
- 4.5. AMBER PRMTOP topology parser
- 4.6. CRD topology parser
- 4.7. GRO topology parser
- 4.8. PDB topology parser
- 4.9. Primitive PDB topology parser
- 4.10. PDBQT topology parser
- 4.11. PQR topology parser

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