AMBER Archive (2008)

Subject: RE: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS)

From: Matthew Tessier (matthew.tessier_at_gmail.com)
Date: Tue Aug 05 2008 - 10:07:22 CDT

Hi,

You can actually use GLYCAM 06 for all parts of an LPS even in a lipid
bilayer.

 

Tessier, M.B., et al. Extension of the GLYCAM06 Biomolecular Force Field to
Lipids, Lipid Bilayers and Glycolipids. Molecular Simulation, 2008. 34(4):
p. 349-364.

 

I'd suggest downloading the latest version of Glycam 06 (e) from the website
<http://www.glycam.com> www.glycam.com to make sure that all parameters are
up to date.

 

Matthew Tessier

 <mailto:mbt3911_at_uga.edu> mbt3911_at_uga.edu

 <mailto:matthew.tessier_at_gmail.com> matthew.tessier_at_gmail.com

Woods' Lab Room 1092

Complex Carbohydrate Research Center - University of Georgia

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Wenyong Tong
Sent: Tuesday, August 05, 2008 10:52 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Need help with force field parameters for
Lipopolysaccharide (LPS)

 

Hello,

For sugar part, you can use glycam04 or 06. For lipid tail,you can use
gaff.

Wenyong

 

 

----- Original Message ----
From: dipti lele <diptisl86_at_gmail.com>
To: amber_at_scripps.edu
Sent: Tuesday, August 5, 2008 6:03:10 AM
Subject: AMBER: Need help with force field parameters for Lipopolysaccharide
(LPS)

Hi everyone!
I'm trying to run a few simulations with LPS but am unable to find a force
field for the molecule. Can anybody please help me with this ? 

-- 

 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu