/usr/share/votca/xml/mapping.xml is in votca-csg-scripts 1.2.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 | <tags>
<item>
<name>name</name>
<desc>
Name of molecule in coarse-grained representation.
</desc>
</item>
<item>
<name>ident</name>
<desc>
Molecule name in reference topology.
</desc>
</item>
<item>
<name>topology</name>
<desc>
Section containing definition of coarse grained topology of molecule.
</desc>
</item>
<item>
<name>topology.cg_beads</name>
<desc>
Section defining coarse grained beads of molecule.
</desc>
</item>
<item>
<name>topology.cg_beads.cg_bead</name>
<desc>
Definition of a coarse grained bead.
</desc>
</item>
<item>
<name>topology.cg_beads.cg_bead.name</name>
<desc>
Name of coarse grained bead.
</desc>
</item>
<item>
<name>topology.cg_beads.cg_bead.type</name>
<desc>
Type of coarse grained bead.
</desc>
</item>
<item>
<name>topology.cg_beads.cg_bead.mapping</name>
<desc>
Mapping scheme to be used for this bead (specified in section mapping) to map from reference system.
</desc>
</item>
<item>
<name>topology.cg_beads.cg_bead.beads</name>
<desc>
The beads section lists all atoms of the reference system that are mapped to this particular
coarse grained bead. The syntax is RESID:RESNAME:ATOMNAME, the beads are separated by spaces.
</desc>
</item>
<item>
<name>topology.cg_bonded</name>
<desc>
The cg_bonded section contains all bonded interaction of the molecule. Those can be bond, angle or dihedral.
An entry for each group of bonded interaction can be specified, e.g. several groups (types) of bonds can be specified.
A specific bonded interaction can be later on addressed by MOLECULE:NAME:NUMBER, where MOLECULE is the molecule ID in
the whole topology, NAME the name of the interaction group and NUMBER addresses the interaction in the group.
</desc>
</item>
<item>
<name>topology.cg_bonded.bond</name>
<desc>
Definition of a group of bonds.
</desc>
</item>
<item>
<name>topology.cg_bonded.bond.name</name>
<desc>
Name of the group.
</desc>
</item>
<item>
<name>topology.cg_bonded.bond.beads</name>
<desc>
List of pair of beads that define a bond. Names specified in cg_beads, separated by commas.
</desc>
</item>
<item>
<name>topology.cg_bonded.angle</name>
<desc>
Definition of a group of angles.
</desc>
</item>
<item>
<name>topology.cg_bonded.angle.name</name>
<desc>
Name of the group.
</desc>
</item>
<item>
<name>topology.cg_bonded.angle.beads</name>
<desc>
List of triples of beads that define a bond. Names specified in cg_beads, separated by commas.
</desc>
</item>
<item>
<name>topology.cg_bonded.dihedral</name>
<desc>
Definition of a group of dihedrals. Since the exact functional form does not matter, this combines proper as well as improper dihedrals.
</desc>
</item>
<item>
<name>topology.cg_bonded.dihedral.name</name>
<desc>
Name of the group.
</desc>
</item>
<item>
<name>topology.cg_bonded.dihedral.beads</name>
<desc>
List of quadruples of beads that define a bond. Names specified in cg_beads, separated by commas.
</desc>
</item>
<item>
<name>maps</name>
<desc>
Section containing definitions of mapping schemes.
</desc>
</item>
<item>
<name>maps.map</name>
<desc>
Section for a mapping for 1 bead.
</desc>
</item>
<item>
<name>maps.map.name</name>
<desc>
Name of the mapping.
</desc>
</item>
<item>
<name>maps.map.weights</name>
<desc>
Weights of the mapping matrix. Entries are normalized to 1, number of entries must match the number of reference beads in a coarse-grained bead.
</desc>
</item>
</tags>
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