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
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 23 2010 - 15:30:09 PDT
