The implicit solvent methods typically do not work well for glycans.
At the very least, they tend to get the rotamer populations wrong.
On Tue, Jun 26, 2012 at 7:11 AM, Kepa K. Burusco <kekoburgo.yahoo.es> wrote:
> [26-VI-2012]
>
> Hi everybody,
>
> I am running series of calculations for glucose anomers in different ways: a) in explicit solvent TIP3P, b) in vacuo, and c) in implicit solvent.
>
>
> For the implicit solvent in part c) I will be using Generalised Born Solvation Model, however "igb" options rank from 1 to 10!!! In oder to decide which is the best value, I have been reading through the GLYCAM_06 paper [J.Comput.Chem.2008.29(4).622-655] and also "ambertools12" and "amber12" manuals, but they don't say so much especifically about GLYCAM focefield and GB models.
>
> Does anyone have any experience with this point? Any advice is welcome.
>
> (I am using amber11, ambertools12 and GLYCAM_06h Force Field)
>
>
> Thank you very much.
>
> Kepa K. Burusco
>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Jun 26 2012 - 10:00:02 PDT
