We have KDO in progress. The person who is handling it is out of the
country at the moment and has limited internet access. I'll write
when I know more.
You could also do as Francois suggests. Either way, you should do
some validation of the structures as they will be new.
On Thu, Feb 2, 2012 at 2:34 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Camille,
>
> For KDO (3-Deoxy-D-manno-oct-2-ulosonic acid), you could adopt two
> different strategies. Is KDO involved in a polysaccharide chain with
> many other regular sugars handled by the Glycam force field?
>
> -1 If "Yes", I think your best bet is to try to develop a KDO fragment
> in agreement with the other available units in the latest version of
> the Glycam force field... In this case, you need to fit the charges
> from a KDO based molecule to generate this KDO fragment in agreement
> with Glycam. You could use R.E.D. Server for that and select the
> 'RESP-C2' charge model "compatible" with GLYCAM.
> See http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
>
> -2 If the answer is "No", another approach would be to derive charges
> and generate FF libraries for your entire KDO-based-oligosaccharide or
> -glycoconjugate by splitting your whole molecule into elementary
> building blocks. You can find several examples of such an approach in
> R.E.DD.B.
> http://q4md-forcefieldtools.org/REDDB/projects/F-71/
> http://q4md-forcefieldtools.org/REDDB/projects/F-72/
> The advantage of this approach is that charges are derived using a
> highly homogeneous approach in a single R.E.D. job involving multiple
> molecules, multiple conformations and multiple orientations depending
> on the user choice. Here, I would start once again by the 'RESP-C2'
> charge model. You could also try to develop another/your own charge
> derivation approach in this case...
>
> Finally, you do not have to 'stick' to the "prep" force field library
> file format... Other file formats are available, which are far more
> advantageous. See for instance:
> http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
>
> regards, Francois
>
>
>> 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?
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 02 2012 - 09:30:03 PST
