What is needed

Before running NAMD, explained in section 9, the following are be needed:

• A CHARMM force field in either CHARMM or X-PLOR format.
• An X-PLOR format PSF file describing the molecular structure.
• The initial coordinates of the molecular system in the form of a PDB file.
• A NAMD configuration file.

NAMD provides the psfgen utility, documented in Section 4, which is capable of generating the required PSF and PDB files by merging PDB files and guessing coordinates for missing atoms. If psfgen is insufficient for your system, we recommend that you obtain access to either CHARMM or X-PLOR, both of which are capable of generating the required files.