Ispopetide bond

From: Milica Utješanović (
Date: Fri Oct 02 2015 - 14:30:04 CDT

Hi all,

I was wandering how it would be possible to patch two structures (two
poli-peptide chains that are built in Molefacture plugin), where one chain
has two N-termini, because it is actually going to be bonded with the other
one through Lys side chain.

I renamed N from the end of Lys's side chain (originally was NZ) and entire
residue (but kept same atom type NH1 as for N-terminal, so I can later use
the existing parameters). My problem is, essentially, that these two
residues are not next to each other, and in topology file +N is next
residue (and -C represent C from the residue before). Also, since this is
isopeptide bond, how important is planarity of it?

Any help is appreciated!

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