RE: carbohydrates: CHARMM versus AMBER

From: Matthew Tessier (mbt3911_at_uga.edu)
Date: Thu Oct 30 2008 - 09:43:27 CDT

Dong Xu,
I'm not sure if NAMD has mixed 1-4 scaling, but ideally you would want to
use a mixed 1-4 scaling feature allowing a per-atom or per-residue
assignment of 1-4 scaling factors. I know AMBER is examining this feature
for newer versions but in the meantime, we typically recommend using the 1-4
scaling if you have to use a [protein] force field that requires 1-4 scaling
with GLYCAM06.

>From the AMBER Tools manual:
"For studying carbohydrate-protein interactions, we suggest that the SCEE
and SCNB scaling factors be set to the appropriate value according to the
protein force field that is chosen. While this would degrade the accuracy of
the rotational populations for free oligosaccharides, it does not appear to
interfere significantly with the stability or structure of protein-bound
carbohydrates, which have inherently reduced internal flexibility."

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 Dong Xu
Sent: Wednesday, October 29, 2008 7:48 PM
To: Matthew Tessier
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: carbohydrates: CHARMM versus AMBER

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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