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.

Preparing separate PDB files

Many PDB files in the PDB databank contain multiple chains, corresponding to protein subunits, water, and other miscellaneous groups. Protein subunits are often identified by their chain ID in the PDB file. In psfgen, each of these groups must be assigned to their own segment. This applies most strictly in the case of protein chains, each of which must be assigned to its own segment so that N-terminal and C-terminal patches can be applied. You are free to group water molecules into whatever segments you choose.

Chains can be split up into their own PDB files using your favorite text editor and/or Unix shell commands, as illustrated in the BPTI example below. If you are using VMD you can also use atom selections to write pieces of the structure to separate files:

# Split a file containing protein and water into separate segments.
# Creates files named myfile_water.pdb, myfile_frag0.pdb, myfile_frag1.pdb,...
# Requires VMD.
mol load pdb myfile.pdb
set water [atomselect top water]
$water writepdb myfile_water.pdb
set protein [atomselect top protein]
set chains [lsort -unique [$protein get pfrag]]
foreach chain $chains {
  set sel [atomselect top "pfrag $chain"]
  $sel writepdb myfile_frag${chain}.pdb
}

Deleting unwanted atoms

The delatom command described below allows you to delete selected atoms from the structure. It's fine to remove atoms from your structure before building the PSF and PDB files, but you should never edit the PSF and PDB files created by psfgen by hand as it will probably mess up the internal numbering in the PSF file.

Very often the atoms you want to delete are water molecules that are either too far from the solute, or else outside of the periodic box you are trying to prepare. In either case VMD atom selections can be used to select the waters you want to delete. For example:

# Load a pdb and psf file into both psfgen and VMD.
resetpsf
readpsf myfile.psf
coordpdb myfile.pdb
mol load psf myfile.psf pdb myfile.pdb
# Select waters that are more than 10 Angstroms from the protein.
set badwater1 [atomselect top "name OH2 and not within 10 of protein"]
# Alternatively, select waters that are outside our periodic cell.
set badwater2 [atomselect top "name OH2 and (x<-30 or x>30 or y<-30 or>30
                               or z<-30 or z>30)"]
# Delete the residues corresponding to the atoms we selected.
foreach segid [$badwater1 get segid] resid [$badwater1 get resid] {
  delatom $segid $resid
}
# Have psfgen write out the new psf and pdb file (VMD's structure and
# coordinates are unmodified!).
writepsf myfile_chopwater.psf
writepdb myfile_chopwater.pdb