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Adding ligands to my MODEL


I'm trying to add NAD to my modeled protein and keep getting a few errors,
like:  Atom index is out of bounds:     7002     7000

NAD is in ./modlib/top_heav.lib and I have added the symbol "J" to
./modlib/restyp.lib so that NAD can be recognized in my alignment file.
NAD is in my TEMPLATE pdb file and alignment file.

Does anyone have an example alignment and corresponding PDB file that they
used to construct ligands along with the protein model?  I expect that I'm
missing something minor and an example would help.

Many thanks,

Troy Wymore
Pittsburgh Supercomputing Center