Re: [AMBER] parameters for Lys-sugar

From: FyD <>
Date: Fri, 23 Mar 2012 17:11:51 +0100


> Thank you, this is a part of a peptide, attached is the whole
> peptide structure ...

So you might start from a dipeptide:

R.E.D. Server can generate different fragemtnts automatically as well:

regards, Francois

> It's not really even a complete lysine, and the attachment is a bit
> unusual. The proximity of the ring oxygen, the anomeric oxygen and
> the nitrogen -- all just one carbon removed from each other -- might
> make good parameterization tricky. I'll think about it a while and
> ask around in the group. I'll get back to you.
> On Fri, Mar 23, 2012 at 11:06 AM, FyD <> wrote:
>> 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.
>> See
>> 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 - 09:30:03 PDT
Custom Search