Hi Lachele,
Yes it does work! So both zwitterionic Ser and Thr have parameters in
GLYCAM_06j-1
for O-glycosylation.
Thanks,
Yun
On Mon, May 8, 2017 at 2:32 PM, Lachele Foley <lf.list.gmail.com> wrote:
> Use the ZOLS residue (ZOLS stands for zwitterion O-linked serine). We
> don't have every relevant amino acid, but we have that one.
>
> You should be able to use something like the following. Here, I assume you
> want to attach a beta-D-glucopyranos to a zwitterionic serine:
>
> source leaprc.protein.ff14SB
> source leaprc.GLYCAM_06j-1
> m = sequence { ZOLS 0GB }
>
> Then, just save whatever files you normally would. Let me know if that
> doesn't work.
>
>
>
> On Sun, May 7, 2017 at 11:25 PM, yunshi11 . <yunshi09.gmail.com> wrote:
>
> > Dear all,
> >
> > I understand that you can easily build glycoprotein or glycopeptide in
> LEaP
> > of AMBERTOOLS, using Glycam_06 and Amber ff12SB/ff14SB force fields. But
> > how about sugars linked to a single amino acid in a way analogous to
> > glycosylation?
> >
> > For a single Serine (linked via O-glycosylation to a sugar residue) , I'd
> > like to have both N-terminal and C-terminal present (i.e. -NH3+ and
> -COO-),
> > but the official Glycam libraries (GLYCAM_amino_06j_12SB,
> > GLYCAM_aminoct_06j_12SB, GLYCAM_aminont_06j_12SB) only contain those for
> > either N-term or C-term residues, not both.
> >
> > So is there a library for glycosylation on single amino acids? Has anyone
> > seen publications on parameters for such molecules?
> >
> > Best regards,
> > Yun
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
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>
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Received on Mon May 08 2017 - 15:30:02 PDT
