Re: carbohydrates: CHARMM versus AMBER

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Wed Oct 29 2008 - 18:47:49 CDT

Hi Matt,

I was wondering how you handle the 1-4 scaling factors (SCEE/SCNB)
when using NAMD and Amber/Glycam06 to simulate the
carbohydrate/protein complex.

Amber requires SCEE=1.2/SCNB=2, but Glycam06 requires 1 for both
factors. Is there a way to take care of this discrepancy in NAMD?

And what do people do when they use Sander or PMEMD?

Thanks a lot!

Dong Xu

On Wed, Jul 2, 2008 at 6:02 AM, Matthew Tessier <mbt3911_at_uga.edu> wrote:
> 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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