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

From: mish <smncbr.gmail.com>
Date: Sat, 25 Jun 2011 18:18:41 +0200

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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jun 25 2011 - 09:30:03 PDT
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