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?
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Received on Thu Feb 02 2012 - 00:00:02 PST
