Re: Topology for lysine bouding in Epsilon

From: Jean-Patrick Francoia (
Date: Wed May 07 2014 - 04:40:11 CDT

Le 06/05/2014 21:04, Kenno Vanommeslaeghe a écrit :
> 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".

Ok, I found the DISU patch:

PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and
                        ! use in a patch statement
                        ! follow with AUTOgenerate ANGLes DIHEdrals command
ATOM 1CB CT2 -0.10 !
ATOM 1SG SM -0.08 ! 2SG--2CB--
ATOM 2SG SM -0.08 ! -1CB--1SG
ATOM 2CB CT2 -0.10 !
IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000
IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000

Just one last question. Do I have to write a patch for each epsilon
bound, with the corresponding numbers of the Lys residues, or can it be
applied more generally ? Because I don't have only one or two epsilon
bonds in my polymer (more like 200).

Thanks in any case for your help.


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