Re: [AMBER] Glycam Parameters for O-SIALIC ACID

From: Lachele Foley (Lists) <"Lachele>
Date: Mon, 27 Jun 2011 17:21:18 -0400

I'm sorry, but I do not fully understand what you need. Are you
saying that you need N-acetyl neuraminic acid or that it is close to
the structure you need? If NeupNac (Neup5Ac) is what you need, then
those residues will do.
 If not, unless you want to develop the ensemble averaged charges, I
need to know exactly the chemical structure you have in mind before I
can help you.



On Sat, Jun 25, 2011 at 12:18 PM, mish <smncbr.gmail.com> wrote:
> I was looking for GLYCAM06 carefully and I can see there are some residues
> 0SA, 7SA 8SA and so on. I think these are the structure I need but I have to
> compare them properly. This was he reason I did not tried further
> in preparing parms suing the suggested approaches. I would definitively
> write you back if I have to go through this approach.
> Can you direct me where can I find the structure of those residues in GLYCAM
> ?
>
> Sincerely
> Mish
>
> On Sat, Jun 25, 2011 at 2:49 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
>
>> Have they made it easier to do ensemble averaging? The last time we
>> checked them out, it wasn't easy to generate proper GLYCAM charges
>> there.
>>
>>
>> On Sat, Jun 25, 2011 at 1:46 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>> > Dear mish,
>> >
>> >> I tried to have a look but I can not find if it is parametrized as one
>> >> residue.
>> >> What could be suggested alternative fregmnets which can be joined (from
>> >> GLYCAM_06) to make O-SIALIC ACID residue ?
>> >
>> > You might look at examples in R.E.DD.B.
>> > See http://q4md-forcefieldtools.org/REDDB/download.php
>> > - http://q4md-forcefieldtools.org/REDDB/projects/F-71/
>> > Gouin et al. J. Org. Chem. 2007, 72, 9032-9045
>> > - http://q4md-forcefieldtools.org/REDDB/projects/F-72/
>> > Abel et al. J. Phys. Chem. B, 2011, 115, 487499
>> > - http://q4md-forcefieldtools.org/REDDB/projects/F-84/
>> > Gouin et al. ChemBioChem, 2010, 11, 1430-1442
>> > - http://q4md-forcefieldtools.org/REDDB/projects/F-85/
>> > Cezard et al. Phys. Chem. Chem. Phys. 2011, in press.
>> >
>> > In these projects you will find information about how to construct new
>> > units for glycoconjugates, and how to set up constraints during the
>> > charge fitting step to generate a new sugar fragment compatible with
>> > previously existing ones.
>> >
>> > regards, Francois
>> >
>> >
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> :-) Lachele
>> Lachele Foley
>> CCRC/UGA
>> Athens, GA USA
>>
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>



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Jun 27 2011 - 14:30:06 PDT
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