File Forms

On-disk molecular structure, trajectory, and topology file formats supported by MolSysMT.

Form	Description
bcif	Binary CIF structure file format
bcif.gz	Gzip-compressed Binary CIF structure file format
cif	Crystallographic Information Framework (CIF/mmCIF) file format
cif.gz	Gzip-compressed CIF/mmCIF structure file format
crd	CHARMM coordinate card (CRD) file format
dcd	CHARMM/NAMD binary trajectory (DCD) file format
fasta	FASTA biological sequence file format
gro	GROMACS coordinate and velocity (GRO) file format
h5	Generic Hierarchical Data Format (HDF5) container file
h5msm	MolSysMT native HDF5 molecular system file format
inpcrd	AMBER ASCII coordinate/restart (inpcrd) file format
mdcrd	AMBER ASCII trajectory (mdcrd) file format
mol2	Tripos MOL2 molecular structure file format
molsys_yaml	Human-authored declarative YAML molecular system file
pdb	Protein Data Bank (PDB) format file
pir	PIR/NBRF sequence file format
prmtop	AMBER molecular topology and parameter (prmtop) file format
psf	CHARMM Protein Structure File (PSF) topology format
smi	SMILES chemical structure line-entry (.smi) file format
structures_yaml	Human-authored declarative YAML structures file
top	GROMACS topology definition (TOP) file format
topology_yaml	Human-authored declarative YAML topology file
trjpk	Packaged trajectory archive file format
xtc	GROMACS compressed binary trajectory (XTC) file format
xyz	MolSysMT ASCII XYZ Cartesian coordinate file format
xyznpy	NumPy binary array coordinate file format