/usr/share/votca/xml/topol.xml is in votca-csg-scripts 1.4.1-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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<DESC>The XML topology root element, the base for the topology can be defined by the "name" attribute</DESC>
<h5md_particle_group>
<DESC>Attribute name holds the name of particles group in H5MD file</DESC>
</h5md_particle_group>
<molecules>
<DESC>The the molecules in the trajectory or other operation on the molecules.</DESC>
<molecule>
<DESC>
Definition of the molecule, with attributes: name, nmols and nbeads.
The name defines residue name, nmols tells how many times this molecule
has to be replicated to match with trajectory file and nbeads
defines number of beads in every molecule.
</DESC>
<bead>
<DESC>
Define the bead in the molecule. Attributes are:
name - the name of bead, type - the type of bead,
mass - the mass of bead and q - the value of charge.
</DESC>
</bead>
</molecule>
<clear>
<DESC>Clear the information about the molecules</DESC>
</clear>
<rename>
<DESC>
Rename the molecules; attributes: "name" - the new name, "range" - the range where the new name will be set
in the format start_range:end_range
</DESC>
</rename>
<define>
<DESC>
Define the molecules; attributes: "name" - the name of molecule, "first" - the id of first molecule, "nbeads" - the number of
beads in the molecule, "nmols" - the number of molecules
</DESC>
</define>
</molecules>
<bonded>
<DESC>This section defines the topology of the molecules, it is used to generate proper exclusions for calculating rdfs</DESC>
<bond>
<DESC>Describes the bond</DESC>
<name>
<DESC>The name of the bond</DESC>
</name>
<beads>
<DESC>
The pair of the beads in the format MOLECULE_NAME:BEAD_NAME
</DESC>
</beads>
</bond>
<angle>
<DESC>Describes the angle</DESC>
<name><DESC>The name of the angle</DESC></name>
<beads>
<DESC>The triplet of the beads in the format MOLECULE_NAME:BEAD_NAME</DESC>
</beads>
</angle>
<dihedral>
<DESC>Describes the dihedrals</DESC>
<name><DESC>The name of the dihedral</DESC></name>
<beads>
<DESC>The quadruplet of the beads in the format MOLECULE_NAME:BEAD_NAME</DESC>
</beads>
</dihedral>
</bonded>
<beadtypes>
<DESC>Allows defining bead types</DESC>
<rename>
<DESC>Rename the bead type; attributes: "name" - the old name, "newname" - the new name</DESC>
</rename>
<mass>
<DESC>Define the mass of the bead type; attributes: "name" - the bead type name, "value" - the new mass</DESC>
</mass>
</beadtypes>
</topology>
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