The 'psfgen' plugin is a structure building tool consisting of a library of portable structure and file manipulation routines that implement Tcl interface, callable from within VMD.

File Formats

The 'psfgen' plugin reads standard PDB files, Charmm topology files, and PSF files in X-PLOR/NAMD format. Psfgen will accept PSF files using the Charmm CMAP cross-term map force field extension. Psfgen does not currently support Charmm PSF files using the Charmm 'EXT' expanded format, but will updated soon.

Generating a Protein Structure File (PSF) - A quick introduction to using psfgen is available as part of the NAMD tutorial.
"Building Gramacidin A" - A NAMD structure building tutorial
psfgen User's Guide (PDF)

Flowchart indicating the role of files as used by VMD, NAMD, and psfgen