Lachele and Francois,
Thanks for your advice! I'm kind of already doing your first suggestion in
a rough way. My project is really in the preliminary stages and we are
just trying to get a protocol down to be able to generate monolayer
lipopolysaccharide surfaces on water slabs. We will need to work on the
forcefield for the whole LPS since there are many components to it that are
not specified in the GLYCAM parameters, but this optimization/validation
will happen after we get the basics down. I was just curious if there was
a KDO unit available since I thought it's inclusion in the AmberTools
manual meant that it would be already developed, and I was afraid I was
overlooking something since I've just started using AMBER. However if KDO
does get released eventually, I would definitely love to know since it will
save my lab a lot of time in the distant future.
Cheers,
Camille
On Thu, Feb 2, 2012 at 9:11 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> 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
>
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>
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Received on Thu Feb 02 2012 - 14:00:02 PST
