Thanks Lachele, I will investigate this more like you suggest.
Lekpa
On 9/9/10, Lachele Foley (Lists) <lf.list.gmail.com> wrote:
> 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 - 10:00:03 PDT
