Re: [AMBER] parameters for Lys-sugar

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Fri, 23 Mar 2012 16:26:19 +0100

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

/Urszula
______________________________________
Von: Lachele Foley (Lists) [lf.list.gmail.com]
Gesendet: Freitag, 23. März 2012 16:11
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for Lys-sugar

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 <fyd.q4md-forcefieldtools.org> 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 http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
>
> or, you might decide to split your molecules into two parts; a glyco
> part and a AA part...
>
> regards, Francois
>
>
>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Mar 23 2012 - 09:00:02 PDT
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