RE: carbohydrates: CHARMM versus AMBER

From: Matthew Tessier (mbt3911_at_uga.edu)
Date: Wed Jul 02 2008 - 08:02:24 CDT

Gianluca,
A literature review comparing the most recent carbohydrate force fields is
not available at this time. The GLYCAM carbohydrate force field has been
developed to be independent of the AMBER simulation program and has been
used with NAMD by the Woods' group for lipid simulations since NAMD allows
you to use AMBER and CHARMM input files.

I encourage you to use the GLYCAM website, www.glycam.com, which includes a
carbohydrate structure builder that allows you to download files in the
AMBER file format. The latest version of the GLYCAM06 force field is also
available on the website and please contact the Woods' group for questions
about the force field development.

GLYCAM06 References:
Karl N. Kirschner, Austin B. Yongye, Sarah M. Tschampel, Jorge
González-Outeiriño, Charlisa R. Daniels, B. Lachele Foley, Robert J. Woods.
GLYCAM06: A generalizable biomolecular force field. Carbohydrates. 2008.
Journal of Computational Chemistry. 29 (4) pages 622 - 655.

Matthew B. Tessier, Mari L. DeMarco, Austin B. Yongye, Robert J. Woods.
Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers
and glycolipids. 2008. Molecular Simulation. 34 (4) pages 349 - 364.

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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Gianluca Interlandi
Sent: Friday, June 27, 2008 6:16 PM
To: NAMD list
Subject: namd-l: carbohydrates: CHARMM versus AMBER

Dear all,

Does anybody have experience simulating carbohydrates with NAMD? In
particular,
I'm interested whether the CHARMM or the AMBER force field is more accurate
to
simulate carbohydrates. I want to simulate a protein attached to mannose.

Any help would be appreciated.

Thanks,

      Gianluca

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                      +1 (206) 685 4435
                      +1 (206) 714 4303
                      http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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