Topology¶
Format |
Description |
Attributes read |
Attributes guessed |
---|---|---|---|
DL_Poly CONFIG file |
names |
masses, types |
|
CHARMM CARD file |
names, resnames, tempfactors |
masses, types |
|
LAMMPS data file |
angles, bonds, charges, dihedrals, impropers |
||
DESRES Molecular Structure file |
atomnums, bonds, chainIDs, charges, names, resnames |
types |
|
GAMESS file |
atomiccharges, names |
masses, types |
|
GROMACS structure file |
names, resnames |
masses, types |
|
HOOMD GSD file |
angles, bonds, charges, dihedrals, impropers, names, radii, resnames |
||
DL_Poly HISTORY file |
names |
masses, types |
|
FHI-aims input file |
elements, names |
masses, types |
|
LAMMPS ascii dump file |
masses |
||
MMTF file |
altLocs, bfactors, bonds, charges, icodes, models, names, occupancies, resnames |
masses |
|
Tripos MOL2 file |
bonds, charges, names, resnames |
masses |
|
ParmEd Structure |
altLocs, angles, bonds, chainIDs, charges, cmaps, dihedrals, elements, epsilon14s, epsilons, gbscreens, impropers, names, nbindices, occupancies, resnames, rmin14s, rmins, solventradii, tempfactors, ureybradleys |
||
Standard PDB file |
altLocs, bonds, chainIDs, elements, icodes, names, occupancies, record_types, resnames, tempfactors |
masses, types |
|
PDBQT file |
altLocs, charges, icodes, names, occupancies, record_types, resnames, tempfactors |
masses |
|
PQR file |
charges, icodes, names, radii, record_types, resnames |
masses, types |
|
CHARMM, NAMD, or XPLOR PSF file |
angles, bonds, charges, dihedrals, impropers, names, resnames |
||
AMBER topology file |
angles, bonds, charges, dihedrals, impropers, names, resnames, type_indices |
||
GROMACS run topology file |
angles, bonds, charges, dihedrals, impropers, molnums, moltypes, names, resnames |
||
Tinker file |
bonds, names |
masses |
|
HOOMD XML file |
angles, bonds, charges, dihedrals, impropers, radii |
||
Extended PDB file |
altLocs, bonds, chainIDs, icodes, names, occupancies, record_types, resnames, tempfactors |
masses, types |
|
XYZ file |
elements, names |
masses, types |