This plugin reads and displays molecular structure files in several formats using the Babel program to translate them into PDB files which are easily read by VMD. In order to use this plugin Babel 1.6 must be installed on your computer and must be executable in your default command path so that the Babel plugin can run it via calls to system(). Babel 1.6 is available from the OpenEye Babel web site

This table lists all of the molecule file formats that Babel will translate to the PDB format which can be loaded by VMD:

Alchemy AMBER PREP Ball and Stick
Biosym .CAR Boogie Cacao Cartesian
Cambridge CADPAC CHARMm Chem3D Cartesian 1
Chem3D Cartesian 2 CSD CSSR CSD FDAT
CSD GSTAT Free Form Fractional GAMESS Output
Gaussian Z-Matrix Gaussian Output Hyperchem HIN
Mac Molecule Macromodel Micro World
MM2 Input MM2 Ouput MM3
Mopac Cartesian Mopac Internal Mopac Output
ShelX Sybyl Mol
Sybyl Mol2 XYZ


This plugin is used only to read files. VMD does not currently support writing to these formats.

Unused data
Babel performs a reasonable translation in most cases, however it is unavoidable that some formats may contain information which doesn't have a corresponding record in PDB files, so this information may be lost in the translation, and thus unavailble when loaded into VMD.

Compressed files
Compressed files will need to be expanded before this plugin can read them.