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

From: Lachele Foley (Lists) <"Lachele>
Date: Tue, 28 Jun 2011 13:51:29 -0400

Ok! :-) Let me know if you need any further assistance.


On Tue, Jun 28, 2011 at 12:19 PM, mish <smncbr.gmail.com> wrote:
> Thanks, Yes, I wanted to see the the structures of N-acetyl neuraminic acid
> in glycam. I looked in the X-RAY structure and it looked like N-acetyl
> neuraminic acid but the confusion created because of incorrect label in
> PDB database, the structure is exactly sialyllactose. all the three residues
> (*A-D-Neu5Ac-(2-3)-B-D-Galp-(1-4)-B-D-Glcp-(1-1)-OH*) are available in
> GLYCAM. Sorry for the confusion.
>
> Sincerely
> Mish
>
> On Mon, Jun 27, 2011 at 11:21 PM, Lachele Foley (Lists)
> <lf.list.gmail.com>wrote:
>
>> 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
>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
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>> >> > 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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-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Jun 28 2011 - 11:00:05 PDT
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