Re: carbohydrates: CHARMM versus AMBER

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Jun 27 2008 - 17:44:41 CDT

Dear Gianluca,

I don't have much experience with carbohydrates, but a few colleagues
of mine have told me that AMBER is usually good for the simulation of
carbohydrates. This opinion, of course, is too biased, so you should
take a look at this paper:

http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-177-2_4

Hopefully it'll help you to figure out which force field would be the
most suitable for your problem.

Cheers,
Michel

On Fri, Jun 27, 2008 at 9:16 PM, Gianluca Interlandi
<gianluca_at_u.washington.edu> wrote:
> 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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