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

From: Lachele Foley (Lists) <"Lachele>
Date: Sat, 25 Jun 2011 08:49:42 -0400

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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> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Jun 25 2011 - 06:00:04 PDT
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