Re: [AMBER] parameters for Lys-sugar

From: FyD <>
Date: Fri, 23 Mar 2012 16:06:35 +0100

Dear Urszula,

> I have a peptide with a sugar bound (beta-D-Glucose), and I would
> like to run MD on that with a protein later. I am trying to find a
> easy way to
> generate the parameters for this part. I know that I could use a
> RESP-A1A charge model for the entire new residue and scaling factors
> for 1-4 interactions.
> However I have no idea how to start with that ...
> I was wondering if there is any tutorial for that?
> Could anyone suggest me something? I attached a mol2 file of the
> residue with sugar bound.

Does this Lys-Glc belongs to a peptide? if yes, this likely means you
need a central fragment for this modified amino-acid. You might decide
to start from a dipeptide; i.e. ACE-AA*-NME; AA* is your modified
amin-acid; i.e. Lys-beta-D-Glucose.


or, you might decide to split your molecules into two parts; a glyco
part and a AA part...

regards, Francois

AMBER mailing list
Received on Fri Mar 23 2012 - 08:30:05 PDT
Custom Search