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4. Topology modules

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4.2. Common functions for topology building — MDAnalysis.topology.core

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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.