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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]] 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]<mailto:[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<https://maps.google.com/?q=296,+1280+Main+St.+W.,+Hamilton,+ON+L8S+4L7,+Canada&entry=gmail&source=g>
Email: [log in to unmask]<mailto:[log in to unmask]> ; Tel: +1(647) 629-1562<tel:(647)%20629-1562>
===========================================================

From: Neha S. Gandhi<mailto:[log in to unmask]>
Sent: December 6, 2017 11:42 PM
To: [log in to unmask]<mailto:[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]<mailto:[log in to unmask]>
CRICOS No 00213J





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