Re: Topology for lysine bouding in Epsilon

From: Kenno Vanommeslaeghe (
Date: Mon May 05 2014 - 15:07:31 CDT

A branched polymer is somewhat more complicated than a "non-traditional
residue". In the carbohydrate force field (those other branched polymers),
the RESIdues are *not* linked when generated, and need to be patched
together with patches that specify the linkage type (1-4, 1-6, 1-3,...)
this allows one to specify all the monomers in a branched polysaccharide
as a linear sequence, and straightforwardly apply complex bonding and
branching patterns within that sequence.
That said, your case sounds considerably simpler, so it will probably be
easier for you to generate each branch as a linear chain of normal
CHARMM36 RESI LYS monomers, then graft the branches using a 2-residue PRES
(which you need to put together yourself). In case you have been following
this list the last few days: what you'd want to do is very similar to what
Sadegh Faramarzi Ganjabad is trying to accomplish.

On 05/05/2014 01:11 PM, Jean-Patrick Francoia wrote:
> Hello,
> I'm new to NAMD, and as far I undestood, if I want to minimize a structure
> with "non traditional residues", I need a topology file for those.
> I'm trying to minimize a homopolymer of lysine, but the lysines can either
> be stitched by their alpha amine or their epsilon amine, giving a branched
> polymer. Is there a topology file for that already built ?
> Regards

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