Thanku Francois, I will try to use RED also... will follow those tutorials and see what I will get
/Urszula
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Freitag, 23. März 2012 17:11
An: AMBER Mailing List
Betreff: Re: [AMBER] parameters for Lys-sugar
Urszula,
> Thank you, this is a part of a peptide, attached is the whole
> peptide structure ...
So you might start from a dipeptide:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
R.E.D. Server can generate different fragemtnts automatically as well:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
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 <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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Mar 24 2012 - 14:00:02 PDT
