Just a quick note to add to Lachele's reply : more recent gb models in
Amber have not included oligosaccharides in parameter training. For
example, with igb=8 we have published training results for proteins and for
nucleic acids. There is no reason to expect it would work well for
oligosaccharides. On the other hand, a quick web search for glycam and
implicit-solvent turned up quite a few hits the you may want to
investigate.
On Jul 24, 2016 10:27 PM, "Lachele Foley" <lf.list.gmail.com> wrote:
> We haven't found that any of the implicit models do very well with
> oligosaccharides. My best advice is to try them all and see which one best
> models the systems of interest to you. If any comes close enough for your
> needs, then use it. You'll need to include this validation in any papers
> you publish about the work.
>
>
>
> On Sun, Jul 24, 2016 at 8:58 PM, yunshi11 . <yunshi09.gmail.com> wrote:
>
> > Hi mailing list,
> >
> > I'd like to run MD for a polysaccharide and check how stable some
> > inter-residue interactions are. Due to limitation of computational
> > resources, I am thinking of using implicit solvent with Glycam force
> field.
> >
> > Would this significantly undermine the accuracy since polar interactions
> > between sugar hydroxyl groups and water molecules are no longer modelled
> by
> > implicit solvent? Is there another way to get better accuracy and
> > performance with limited resources?
> >
> > Thanks for any suggestion.
> >
> > Yun
> > _______________________________________________
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> > 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 Mon Jul 25 2016 - 04:30:02 PDT
