Hi thanks a lot for offering the help.
I would like to mention that basically I am doing free energy calculation
for protein/saccharide complexes using LIE approach. I got interesting
result for mono-saccharides but most of the tri-saccharide appeared
as outliers. The reason I can assume is its interaction energies in water,
because the confirmation of sugar reported in reported with crystal
structure may not the the minimum energy confirmation in water. Whereas
getting the minimum energy confirmation in water is a complex problem like
peptide folding. yesterday, I looked at 3D-BAO database for saccharides and
they says that the available confirmation in the DB is minimum energy
confirmation. For the time being I am think to use those structure for
water simulation but definitely I would like to on this problem of
confirmation sampling for sugars. Let me finish my this task/article and
then i will let you know when I start the this work, Its seems challenging
and we can try GLYCAM 06 with reported methods to see how this force filed
influence that results.
...Sushil
On Fri, Sep 24, 2010 at 3:40 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> I might not be able to answer this well for a day or three. If
> someone else wants to take it, feel free.
>
> People have done this sort of thing a lot. Have you done a literature
> search? Check procedures for molecules other than just trisaccharides
> because most of the technique will be general. We do think it will be
> advantageous to employ the GLYCAM 06 force field, and we can help you
> with that. Literature search terms might include "conformational
> search" or "conformational sampling". You might also try searching on
> "potential energy maps." Al French does a lot of that using MM3. You
> could translate the basics to another force field, e.g., glycam, if
> you like. I might have seen some recent papers that get close to what
> you seek, but I can't get to the list right now to check it.
>
> We could certainly help you to evaluate a procedure (or several
> procedures), but it would be worthwhile for you to see the literature,
> too.
>
> :-) Lachele
>
>
> On Thu, Sep 23, 2010 at 6:21 AM, Sushil Mishra <sushilbioinfo.gmail.com>
> wrote:
> > Hello all,
> >
> > I would like to ask a general question about getting minimum energy
> > conformational structures of tri-saccharides in explicit solvent. Does
> > anyone of you know any method or article where they attempted this
> problem ?
> > My interest is in extracting interaction energies (Vdw and Ele) if
> > tri-saccharides in water, when tri-saccharide is in its minimum free
> energy
> > confirmation.
> >
> > Looking forward to hear from you all.
> >
> >
> > Sincerely
> > Sushil
> > _______________________________________________
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 23 2010 - 22:00:03 PDT
