AMBER Archive (2009)

Subject: RE: [AMBER] Conformation of sulfated Glucosamine

From: Matthew Tessier (matthew.tessier_at_gmail.com)
Date: Wed May 06 2009 - 10:19:22 CDT

Neha,
Two questions come to mind:
1. Are you using the latest version of GLYCAM06 from the website
(www.glycam.com)?
2. Are you comparing to NMR NOEs/J-couplings directly or are you using the
interpretation of the J-couplings/NOEs to determine the chair conformation?
I caution against comparing to their interpretation and not directly to the
values they obtained. You should calculate the same values as the
experiment directly from the MD and use that to compare to the experimental
values.

Matthew Tessier
mbt3911_at_uga.edu
matthew.tessier_at_gmail.com
Woods' Lab Room 1092
Complex Carbohydrate Research Center - University of Georgia

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of Neha Gandhi
Sent: Wednesday, May 06, 2009 5:55 AM
To: amber_at_ambermd.org
Subject: [AMBER] Conformation of sulfated Glucosamine

Hi List,

Did anybody tried running unrestrained dynamics of GlcNS6S using
explicit solvent TIP3P? It has highly stable conformation 4C1
according to NMR but with glycam_06 and resp charges, it fluctuates a
lot. How can it explore other conformations even as monosaccharide or
in longer sequence? Am I missing out something?

Thanks 

-- 
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845

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