(adapted from a tutorial on the NAMD web site)

  I. Files

1. Running a molecular dynamics simulation with NAMD requires five files:
   • A PDB (Protein Data Bank) structure file

   • A PSF (Protein Structure File) connectivity file

   • A force field parameter file

   • A topology file

   • A configuration file, in which the options for running the simulation are set

   The .psf file is necessary because MD programs need bond connectivity information, bond angles, and other similar information that is not contained in the typical .pdb file. This information is obtained from a CHARMm topology file, and combined with the Cartesians in the .pdb file.

   1. The .pdb file can be obtained in three ways:
      • download from the Protein Databank

      • create structure in the PC version of PCModel and save as .pdb

      • translate from a structure in another format using the PC program Mol2mol

   2. The parameter and topology files are in /usr/local/NAMD/params on your workstation

   3. The PSF file is created using VMD, the graphical interface for NAMD, the PDB file, and the topology file.

   4. The configuration file is created by the user, by editing one of several standard configuration files stored in /usr/local/NAMD/configs.