Re: Topology for lysine bouding in Epsilon

From: Kenno Vanommeslaeghe (
Date: Tue May 06 2014 - 14:04:37 CDT

On 05/06/2014 02:38 PM, Jean-Patrick Francoia wrote:
> Why is it a problem a residue can bind on the 2 sides ? Isn't it possible
> to modify the topology file to allow a bond on the main chain and on the
> side chain ?

I don't have time to explain this any further than I did, but if you don't
want to take my word for it, just try it and you'll see.

> Please correct me if I'm wrong, I'm trying to understand how the 2
> residues approach works. You basically define a new residue, with a length
> of n Lysines. Then you modify this residue on a certain amino acid, to
> allow an epsilon bond. Then you create another residue, of a length of m
> Lysines. Then you modify the last one to bond on the carbonyl part. Am I
> right or not yet ?

No, that sounds far too complex and laborious. You would first generate 2
perfectly ordinary peptide chains consisting of perfectly ordinary LYS
residues, then you would use a PRES (patch residue) to patch them
together. Just like you can patch peptide chains together with the
disulfide bond patch (PRES DISU). The patch in question involves a residue
from one chain and another residue from another chain, which requires a
specific syntax in the PRES (atom names starting with numbers). That's why
I call it a "2-residue patch".

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