NAMD uses the same protein structure files that X-PLOR does. At this time, the easiest way to generate these files is using X-PLOR or CHARMM, although it is possible to build them by hand. CHARMM can generate an X-PLOR format PSF file with the command ``write psf card xplor''.
NAMD supports CHARMM19, CHARMM22, and CHARMM27 parameter files in both X-PLOR and CHARMM formats. (X-PLOR format is the default, CHARMM format parameter files may be used given the parameter ``paraTypeCharmm on''.) For a full description of the format of commands used in these files, see the X-PLOR and CHARMM User's Manual .
NAMD produces DCD trajectory files in the same format as X-PLOR and CHARMM. The DCD files are single precision binary FORTRAN files, so are transportable between computer architectures. They are not, unfortunately, transportable between big-endian (most workstations) and little endian (Intel) architectures. (This same caveat applies to binary velocity and coordinate files. The utility programs flipdcd and flipbinpdb are provided with the Linux/Intel version to reformat these files.) The exact format of these files is very ugly but supported by a wide range of analysis and display programs.