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

From: mish <smncbr.gmail.com>
Date: Tue, 28 Jun 2011 18:19:59 +0200

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
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > 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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> >>
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> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Tue Jun 28 2011 - 09:30:03 PDT
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