> I have a protein structure (protein.pdb) and it has a residue called ACA in
> chain C. I have prepared lib file (ACA.lib). Then I describe head and tail
> group of this non standard residue. I saved the file as ACA.lib. I m yet to
> calculate the charges.
>
> I try to load the whole protein after loading the lib file. The N-terminal
> of ACA residue connects well with the previous residue but the C-terminal of
> this residue misses out the connectivity with the N atom of the proceeding
> residue which is MET.
> Well, this residue is connected at the ends with standard amino acid and
> hence if I use the gaff forcefield, it complains about the atom type between
> standard and non standard residue. If I use amber atom type then its
> complains about the N-N bond type wherein no such bond exists in the
> peptide.
Yes I saw examples of such N-N bond in the literature in peptide analogs:
you might look at the work of P. Legrel (Rennes, France)
You need to use the Amber99SB force field/force field atom types.
For this N-N bond, you will have to develop your own FF parameters.
