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Build the glucose with the terminal aglycon (OMe or whatever).  Once you do, at the bottom will be a button for "Add Derivative".  Click that, then click on the DGlcp as the residue to which you want to add derivatives, then choose sulfate and the positions where you want the derivatives.  The builder can't put sulfate at the anomeric position, but it can put it everywhere else.


On Thu, Dec 7, 2017 at 2:48 AM, Neha S. Gandhi <[log in to unmask]> wrote:

Hi Lachele,

 

The site works =).

 

I can build the glucose tetrasaccharide. How can I add sulphate groups to it? for example, in case of GAGs we have sulphate substitution, but in this case, I have glucose. I aim to simulate the oligosaccharide in AMBER.

 

Thanks,

Neha

 

From: Users of GLYCAM & GLYCAM-Web [mailto:[log in to unmask]EDU] On Behalf Of Lachele Foley
Sent: Thursday, 7 December 2017 5:45 PM
To: [log in to unmask]
Subject: Re: sulphated glucose tetrasaccharide

 

Site should work now.  Let us know if you have trouble.

 

http://glycam.org/cb

 

 

On Wed, Dec 6, 2017 at 11:50 PM, Naveen Kumar Vasudevan <[log in to unmask]> wrote:

You can use the Carbohydrates builder, if its a short chain and add substituent groups to it. The website is down right now, but you can access it soon.  This will give you the pdb file.

 

===========================================================
Naveen Kumar Vasudevan, Graduate student,
The Xi Research Lab,
Dept. of Chemical Engineering, McMaster University,
JHE- 296, 1280 Main St. W., Hamilton, ON L8S 4L7, Canada
Email: [log in to unmask] ; Tel: +1(647) 629-1562
===========================================================

 

From: Neha S. Gandhi
Sent: December 6, 2017 11:42 PM
To: [log in to unmask]
Subject: sulphated glucose tetrasaccharide

 

Dear List,

 

I am working on a molecule with B-D-glucose. The OH groups of glucose are substituted by sulphates. How can I prepare a pdb file and amber topology using GLYCAM?

 

Many thanks,

Neha

 

Dr. Neha S. Gandhi  |  Vice-Chancellor’s research fellow

School of Mathematical Sciences and Institute for Health and Biomedical Innovations,

Science and Engineering Faculty | Queensland University of Technology

P-Block, Level 7, Gardens Point Campus
ph 3138 7394| email:
[log in to unmask]
CRICOS No 00213J

 

 



 

--

:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA




--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA