Generates a psf file from the given pdb file. The psf file is written to a filename derived the input filename. Usage: pdb2psf <pdbFile>
options are:
-disulfide_bond sel1 sel2 - specify residues with disulfide bonds.
-selection <sel> - specify a subselection of the full PSF
to convert. Defaults to all atoms.
-topology type file - specify alternate topology file for
the specified seqeunce type. Type is either
protein or nucleic, while file can be path,
or an entry in the toppar directory.
-outfile name - name of generated psf file. The default is to use
the input filename with a ``.psf'' suffix.
-delUnknown - to delete the unknown atoms from
the PDB file before the psf file is been written.
The option is off if not specified.