VMD can use the program Babel, if installed, to translate a wide variety of different molecular data files into the PDB format. Babel, written by Pat Walters and Matt Stahl, can convert between many types of molecular data files. Not all of these have been tested for use with VMD, so your results may vary. Some data formats, such as XYZ, contain a series of coordinates. Babel converts these to a series of PDB files which VMD then reads as an animation. For more information about Babel, see http://www.eyesopen.com/babel.html VMD supports version 1.6 of Babel. Older versions of Babel will not work correctly with VMD.
VMD at present has no provision for using Babel to convert the output PDB CRD, or DCD files to anything else (see sections S, S and S for information on writing output files).
The Babel-VMD interface uses two
environment variables,
VMDBABELBIN
and
VMDTMPDIR.
The first specifies the absolute location for the Babel binary
(i.e. it must include the name of the executable itself, such as
/usr/local/bin/babel (Unix), or C:\Program Files\Babel\babel.exe (Windows)).
The second defines the location for the temporary PDB files made by Babel.