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Ordinary Usage

The psfgen tool is implemented as a Tcl interpreter which reads commands from standard output. You may use loops, variables, etc. as you would in a VMD or NAMD script. You may use psfgen interactively, but we expect it to be run most often with a script file redirected to standard input.

Generating PSF and PDB files for use with NAMD will typically consist of the following steps:

  1. Preparing separate PDB files containing individual segments of protein, solvent, etc. before running psfgen.
  2. Reading in the appropriate topology definition files and aliasing residue and atom names found in the PDB file to those found in the topology files. This will generally include selecting a default protonation state for histidine residues.
  3. Generating the default structure using segment and pdb commands.
  4. Applying additional patches to the structure.
  5. Reading coordinates from the PDB files.
  6. Guessing missing coordinates of hydrogens and other atoms.
  7. Writing PSF and PDB files for use in NAMD.


next up previous contents
Next: List of Commands Up: Creating PSF Structure Files Previous: Creating PSF Structure Files   Contents
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