generate problem

[MBTPING at CCVAX.SINICA.EDU.TW]

Hi, Celine Francart.

The segid is for the last four characters in each atom coordinate record
in PDB files.  If the original protein.pdb or peptide.pdb do not contain
such segid, the 'name' in segment should be left blank, or X-Plor will
not find the atoms in your PDB files.

I would suggest the following:

 segment
   name="    "
   chain
     @TOPPAR:toph19.pep
     coordinates @protein.pdb
   end
 end
 vector do (name="O") ( name OT1 )
 vector do (name="OXT") ( name OT2 )
 vector do (name="CD1") ( name CD and resname ile )
 coordinates @protein.pdb
 vector do (segid="PROT") (segid "    ")

to generate the protein moiety of you complex.  The peptide should b
be generated by similar protocol.

Sincerely,

Ping Ko