Hi! Sorry to take so long responding.
it would be worthwhile modeling the glucose with GLYCAM parameters. We
don't have templates for the cyanogenic aglycon, though.
You might try asking our mailing list about that. There are more folks
paying attention there who might be able to help you with that or who might
have experience with a similar system. You can sign on to the list here:
https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
On Wed, Jul 18, 2018 at 2:51 AM senal dinuka <senal.ichemc.edu.lk> wrote:
> Dear Amber/GLYCAM users,
>
> I am trying to simulate below mentioned ligand (linamarin) docked to
> b-Glucoside enzyme. It is made up of a glucose moiety in which anomeric O-H
> is substituted by a cyanogenic moitey. I would like to know if one would
> necessarily require the use GLYCAM force-field to model such system. If so
> how to prepare the PDB/mol2 file to comply with GLYCAM naming conventions.
>
> 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
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Jul 24 2018 - 09:00:02 PDT
