There are parameters except for the charges. You would need to
generate ensemble-averaged charges for the phosphated residues you
plan to simulate. I understand that the RED server can now do that
for you in a GLYCAM-appropriate manner (I haven't tried it -- if you
do, let me know how it goes!).
Before we can activate the button, we need to work out a set of
general rules for adding phosphates at various locations in glycan
residues. Doing that isn't a trivial task. The sort of rules I'm
talking about are discussed in the How-To at the URL below. Those are
the rules used by the server when someone adds derivatives on the
builder. You don't need to figure out those rules. Like I said, you
just need to get ensemble-averaged charges for the residue(s) of
interest.
http://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/
On Tue, Jun 17, 2014 at 12:26 PM, Raj Schneider
<raj.schneider.uni-dortmund.de> wrote:
> Dear AMBER users and developers,
>
> we want to use the GLYCAM forcefield for phosphorylated carbohydrates. The
> lastest AMBER manual mentions in the table on page 36 that phospate
> parameters exist in the GLYCAM force field, and it seems that there is
> published work "out there" that uses such parameters. However, we could
> not apply the phospate derivate button on the GLYCAM carbohydrate builder,
> whereas the sulfate, acetyl or methyl groups seem to work flawlessly. Can
> we somehow use the builder or do we need to derive our own parameters? Can
> somebody give us a tip on how to get started?
>
> We appreciate your help.
> Raj Schneider & Jochen Heil,
>
> TU Dortmund,
> Germany
>
>
>
>
> _______________________________________________
> 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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Received on Tue Jun 17 2014 - 10:00:02 PDT
