AMBER Archive (2008)

Subject: Re: AMBER: AMBER force field for glycolipid

From: Stephane Abel (Stephane.Abel_at_cea.fr)
Date: Thu Oct 09 2008 - 09:08:49 CDT

Thank you Dr Tessier for your advices

I will read the paper and try the ff.

Matthew Tessier wrote:

> Dr. Abel,
> The GLYCAM06 force field includes lipid parameters that are designed to work
> with the existing GLYCAM06 and GLYCAM04 force fields. I can't speak to
> using the ff force field for the tails, but GLYCAM06 and GLYCAM04 have been
> designed to work with FF99/FF99SB for proteins. The main concern with using
> the GLYCAM and FF force fields is the 1-4 scaling factor. The FF force
> field uses a 1-4 scaling factor while GLYCAM does not. I've included the
> reference for the GLYCAM06 Lipids force field below. Also, you may want to
> consider using the latest version of GLYCAM06 which is available at
> http://www.glycam.com/gl_params.html . These files should be placed in
> their AMBER directories for use.
>
> Tessier, M.B., DeMarco, M.L., Yongye, A.B., Woods, R.J. Extension of the
> GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids.
> Molecular Simulation, 34(4) 2008, pages 349-363.
>
> 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-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Stephane Abel
> Sent: Wednesday, October 08, 2008 8:25 AM
> To: amber_at_scripps.edu
> Subject: AMBER: AMBER force field for glycolipid
>
> Dear AMBERS users
>
>
> For my work, I would like to simulate maltose-glycolipids micelles in
> water. So by searching in the literature I found this paper
>
>
> 1. Chong, T.T., R. Hashim, and R.A. Bryce, Molecular Dynamics
> Simulation of Monoalkyl Glycoside Micelles in Aqueous Solution:
> Influence of Carbohydrate Headgroup Stereochemistry. J. Phys. Chem. B,
> 2006. 110(10): p. 4978-4984.
>
>
> In this article, the authors used the force field from the cornell et
> al. ff for the alkane tail et glycam_2000 for the surfactant headgroup.
> So I would like to compare the micelles structures obtained with AMBER
> ff with those previously performed with CHARMM ff. So my questions are:
>
>
> - Is this combination of ff is well suited for this work ?
>
> - If not, does it exist more recent (i.e. up to date) potential ?
>
>
> Thank you very for your advices
>
>
> Dr Stephane Abel
>
>
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