Re: [AMBER] Converting atom naming to GLYCAM

From: Lachele Foley <>
Date: Tue, 5 Jun 2018 10:55:07 -0400

We have some tools in development, but none currently exist that I know of.

How large is the glycoside? Our naming schemes can be determined by
comparing to our prep file entries. You'd have to make the changes by
hand, but you would have a template.

Find prep file here:
Grab the one at the top of the table. It's just a text file.

On Tue, Jun 5, 2018 at 4:50 AM, senal dinuka <> wrote:

> Dear all,
> I have a cyanogenic glycoside as my ligand which is in sybyl atom typing. I
> thought of using glycam forcefield employed in amber18 to model this
> ligand. I really appreciate if anyone can point me in the direction of a
> tool where I can convert my structure to GLYCAM naming to comply with
> forcefield.
> Regards,
> --
> D L Senal Dinuka
> Grad.Chem., A.I.Chem.C.
> Research Assistant
> College of Chemical Sciences
> Institute of Chemistry Ceylon
> Rajagiriya
> Sri Lanka
> +94 77 627 4678
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Tue Jun 05 2018 - 08:00:03 PDT
Custom Search