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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:
- Preparing separate PDB files containing individual segments of
protein, solvent, etc. before running
psfgen
.
- 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.
- Generating the default structure using segment and pdb commands.
- Applying additional patches to the structure.
- Reading coordinates from the PDB files.
- Guessing missing coordinates of hydrogens and other atoms.
- Writing PSF and PDB files for use in NAMD.
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