We should have KDO in a week or two. Write me off list if interested.
On Thu, Feb 2, 2012 at 7:43 PM, Lachele Foley (Lists) <lf.list.gmail.com> wrote:
> 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?
>>> >
>>> >
>>> >
>>> > _______________________________________________
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>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> :-) Lachele
>>> Lachele Foley
>>> CCRC/UGA
>>> Athens, GA USA
>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Feb 06 2012 - 12:00:04 PST
