Hey Amber masters,
Sorry I meant to say that I need the prep file for a terminal alpha-KDO and
a alpha-KDO with a linkage in the 3 position.
Regards,
Camille Sultana
On Wed, Feb 1, 2012 at 5:06 PM, Camille Sultana <camillesultana.gmail.com>wrote:
> Hi,
>
> I am a new user of Amber, so this may seem like a rather trivial question.
>
> I am trying to build a polysaccharide that includes a KDO unit. According
> to the AmberTools manual I have it appears that GLYCAM-06 should have
> specifications for KDO in the GLYCAM-06.prep file. However when I search
> for the residue code KO it comes up empty. So does anyone know where I
> should look/have KDO prep files? I need one for a terminal beta-KDO and
> one for a beta-KDO with a linkage in the 3 position. I have looked at the
> most recent version of the GLYCAM-06.prep file online as well.
>
> Also since KDO has a two letter code, how do I specify linkages and alpha
> vs beta form in a three letter code?
>
> Thanks,
> Camille
>
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Received on Wed Feb 01 2012 - 17:30:06 PST
