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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>
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Aug 16 2011 - 13:00:03 PDT
