Use the SEQRES info from the PDB file to declare the full sequence (via READ SEQU) in the PSF; be sure to use the SETUP keyword with GENErate. Then use internal coordinates (intcor.doc) to build Cartesian coords for the missing residues--
IC PURGE ! cleanup ic table
IC PARAM ! get any missing bond and angle values from params
IC FILL PRESERVE ! update IC values based on known coords
IC BUILD ! place missing coords
The backbone torsions for the missing residues will be ca. 180 deg.
(This post probably belongs in the "Setup" forum, since it is not a direct question about one of the posted example scripts.)
Last edited by rmv; 11/24/07 06:18 PM.