Molfile Plugin Documentation
Molfile plugins act as translators between the on-disk file
representations of molecular structures, trajectories, volumetric
data sets, and graphics geometry data, and the in-memory
representation of these data in VMD. This page contains a
list of all of the currently available file reader plugins for VMD.
For each plugin, we try to maintain an up-to-date document which
explains what limitations the plugin has, whether it reads all data or
only some of the data from the file format, any known bugs, and any
other useful information, often with links to the file format specifications
which were used to develop the plugin.
Calling VMD molfile plugins from your own code
Although the molfile plugins were primarily developed for use within VMD,
they can also be used by other scientific software written
in C/C++/Fortran. They are provided under the
UIUC Open Source License.
See the
VMD Plugin Programmer's Guide
for more information on using VMD plugins in other software.
Molecule Coordinate/Structure File Plugins
- AMBER 4-6 structure file(.parm)
- AMBER 7-9 structure file(.prmtop, .parm7)
- AMBER 7-9 restart file(.rst7)
- Babel file translator plugin
- Biograf structure files (.bgf)
- Insight II/Discover coordinate file (.car)
- CHARMM coordinate file (.crd)
- CHARMM, CNS, NAMD, X-PLOR PSF structure file (.psf)
- GAMESS log file (.log)
- Gromos 87, Gromacs structure file (.gro)
- Gromos 96, Gromacs coordinate and trajectory (.g96)
- H5MD plugin (.h5)
- NAMD Restart file (.namdbin)
- Insight II/Discover structure file (.mdf)
- MMTK NetCDF structure reader (.nc)
- Molden structure files (.molden)
- PDB (Protein Data Bank) files (.pdb)
- PQR (coordinate, charge, and radii) (.pqr)
- SYBYL Mol2 structure files (.mol2)
- Tinker coordinate and trajectory reader (.arc)
- VASP atomic configurations (.POSCAR, .CONTCAR)
- VMD XBGF structure files (.xbgf)
- VTF structure files (.vsf, .vcf)
- WebPDB (web-based PDB downloader)
- XCrySDen, Quantum Espresso XSF/AXSF coordinate files (.axsf, .xsf)
- XYZ coordinate files (.xyz)
Molecular Dynamics Trajectory File Plugins
Volumetric Data/Density/Potential Map Plugins
- Autodock Grid Map File reader (.map)
- AVS Field File reader (.fld)
- Biomocca volumetric occupancy map reader (.bmcg)
- Brix format electron density map reader (.brix)
- CCP4, MRC format electron density map reader (.ccp4, .mrc)
- Data Explorer (DX) format volumetric grid (.dx)
- Delphi, GRASP unformatted binary phimap reader (.grd, .phi)
- Delphi, GRASP formatted ASCII phimap reader (.big)
- Gaussian "cube" file reader (.cube)
- Molecular Discovery, UHBD GRID map reader (.grid)
- gOpenmol PLT format electron density map reader (.plt)
- "O" DSN6 format electron density map reader (.ds6, .dsn6, .omap)
- Situs volumetric grids (.sit, .situs)
- SPIDER volumetric images (.spi, .spider)
- UHBD potential maps (.uhbd)
- VASP charge densities and electron localization functions (.CHGCAR, .ELFCAR, .LOCPOT, .PARCHG)
- X-PLOR, CNS format electron density map reader (.cns, .edm, .xplor)
- XCrySDen, Quantum Espresso XSF/AXSF trajectory files (.axsf, .xsf)
- XtalView "fsfour" electron density map reader (.fs, .fs4)
Graphics Plugins
