AMBER Archive (2006)

Subject: AMBER: modeling a non-standard molecule.

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Wed Mar 08 2006 - 15:02:50 CST

Dear amber users,
  This is in continuation to my last post about havinng trouble
putting in the non-standard residue back in the protein after modeling
it. I specified the head and the tail atom of the residue to make the
right bonds. But I have another problem now. I can save the prmtop and
inpcrd file for both the non-standard residue and the protein (without
that molecule) separately but when I put the molecule in the protein
and try to crate the prmtop and inpcrd file, it gives me a bunch of
warnings for missing parameters (inlcuding bond lengths, angles and
finally torsions). I think most of these warnings come from the new
bonds that I make between the molecule and the residues on either
side.

Any help would be greatly appreciated.
thanks
Nitin
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