File formats

PDB files

The PDB (Protein Data Bank) format is used to store coordinate or velocity data being input or output from NAMD. This is the standard format for coordinate data for most other molecular dynamics programs as well, including X-PLOR and CHARMM. A full description of this file format can be obtained via anonymous FTP from ftp.pdb.bnl.gov in /pub/format.desc.ps.Z or /pub/format.desc.txt.

X-PLOR format PSF files

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''.

CHARMM19 and CHARMM22 parameter files

NAMD supports CHARMM19 and CHARMM22 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 [5].

DCD trajectory files

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.