After building sugars, there is an option for "Add Derivative". After that, click the sugar you want to add sulfate. Then, choose "Sulfate" as the derivative. Lastly, choose the position for the sulfate.
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.
From: Users of GLYCAM & GLYCAM-Web [mailto:[log in to unmask]]
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.
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
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?
Dr. Neha S. Gandhi | Vice-Chancellorís research fellow
School of Mathematical Sciences and Institute for Health and Biomedical Innovations,
Science and Engineering Faculty | Queensland University of Technology
Athens, GA USA