Re: [AMBER] parameters for Lys-sugar

From: Lachele Foley (Lists) <"Lachele>
Date: Fri, 23 Mar 2012 14:01:27 -0400

My concern isn't so much developing the charges so much as is finding
good parameters for the rest of the force field in the linkage
environment. The anomeric center is complex to model all by itself.
If you add a positively charged group so close by, that's likely to
complicate things more.

For the charges, especially with the tight and complex charge
distribution you have there, I recommend an ensemble average. If you
just use a few structures you might end up with charges that bias the
structure in some manner. I think RED can be used for an ensemble of
structures. Francois can help more with that. We do all ours
in-house, of course. But, the results should be equivalent.

Definitely validate whatever you decide to use. Find experimental
j-couplings or something else that you can calculate from the
structure. This is especially important in your situation. If you
can't find any experimental values, then validate against appropriate
quantum structures.

On Fri, Mar 23, 2012 at 12:11 PM, FyD <> wrote:
> Urszula,
>> 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
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:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Fri Mar 23 2012 - 11:30:02 PDT
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