Apparently, KDO is nearly finished. I can't say now what "nearly"
means, but I will update you.
On Thu, Feb 2, 2012 at 4:53 PM, Camille Sultana
<camillesultana.gmail.com> wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Feb 02 2012 - 17:00:02 PST
