Ordinary Usage

psfgen is currently distributed in two forms. One form is as a standalone program 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. The second form is as a Tcl package which can be imported into any Tcl application, including VMD. All the commands available to the standalone version of psfgen are available to the Tcl package; using psfgen within VMD lets you harness VMD's powerful atom selection capability, as well as instantly view the result of your structure building scripts. Examples of using psfgen both with and without VMD are provided in this document.

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. Deleting unwanted atoms, such as overlapping water molecules.
7. Guessing missing coordinates of hydrogens and other atoms.
8. Writing PSF and PDB files for use in NAMD.