Hi Lachele,
So if I find things not in accordance with experimental data, what can I do
to change it manually?
Is it technically possible to do it due diligence in the first place? That
is, cut the molecule into three parts as I mentioned before, use GLYCAM for
the sugar part, 99SB for the Thr, and GAFF for modified Phe and the
thio-glycosidic linkage. And may I then link these parts together using LEaP
?
Thanks,
Yun
On Tue, Aug 16, 2011 at 12:39 PM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> GAFF should get you a reasonable result. You'd definitely need to do
> some validation to be sure things are working right (check angles or
> H-bonding or whatever you can find experimental values for). You
> might ask if it matters. For example, if you are simulating a tightly
> bound complex, then the glycosidics can't change anyway. If they can
> change, then you need to find some way to determine whether or not the
> method is working. It would take significant work to get Glycam
> working with all parts of this system.
>
>
> On Tue, Aug 16, 2011 at 2:34 PM, Yun Shi <yunshi09.gmail.com> wrote:
> > Hi all,
> >
> > I have a small molecule that consists of a Thr with an ACE cap, a
> modified
> > (CO becomes CH2) Phe, and a rhamnose linked to Phe via a thio-glycosidic
> > linkage. And please see attached the molecule I drew.
> >
> > While the Thr and Rha are the standard building blocks of GLYCAM06 and
> 99SB
> > force fields respectively, what about the modified Phe and the
> > thio-glycosidic linkage?
> >
> > As what seemed to be discussed before in the archive, GAFF can be applied
> to
> > the entire molecule. But the sugar ring is very sensitive to dihedral
> > parameters, right? So the GAFF parameters (and am1-bcc charges) may not
> be
> > good enough for sugar?
> >
> > Thus, I wonder if it's possible to add all the bond, angle, dihedral, and
> > charge parameters for the modified Phe and the thio-glycosidic linkage by
> a
> > .frcmod file. But where can I find proper parameters for thio-glycosidic
> > linkage? Could anyone tell me the steps (formats) to construct such a
> > .frcmod file?
> >
> > Any help is appreciated!
> >
> > Thanks,
> >
> > Yun Shi
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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Received on Fri Aug 19 2011 - 10:00:03 PDT
