I think it's pretty unlikely that they will invert. Just by
inspection, I think the lowest energy path would be a transition
state where the ring oxygen, C1, C2, H1 and OH1 are all planar. I've
asked a couple people in the group if they might be able to get that
energy easily. I suppose you could always build the relevant
structures (at least two, not counting positions of other atoms).
Then, get single-point Amber energies for them and calculate the
temperature needed to get a significant chance of inversion by
comparing to the energy in a normal conformation.
If you really just want to constrain, my initial thought is to
constrain something relatively insignificant to most sugar chemistry,
or at least to the chemistry of interest to you. Since you're doing
REMD, I presume you need sampling, and a restraint will necessarily
affect that. For example, you might choose the H1-C1-C2-H2 torsion.
In order to have anomeric inversion, that torsion would have to change
significantly. But, if you constrain it, you haven't kept the more
chemically important hydroxyls from many motions they might make. In
short... I would probably pick something that is unlikely to impact
the goal of your study, and to use minimal restraints.
On Thu, Sep 9, 2010 at 11:24 AM, Lekpa Duukori <duukori.gmail.com> wrote:
> Hello,
>
> I am performing REMD (max. temperature about 550K) of a glyco-peptide
> and I want to use some restraints to prevent anomeric inversion. I
> have about 20ns of data per replica and I have not seen this happen
> but I just want to be sure it does not happen over a longer timescale.
> The problem is I am not sure exactly how to proceed in making the
> constraint files, i.e what dihedrals to constrain to effect this. The
> sugar in questio is galactose so I use 0LA and 0LB in GLYCAM.
> Any ideas welcome.
>
> Thanks.
>
> Lekpa
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Sep 09 2010 - 09:30:04 PDT
