AMBER Archive (2005)

Subject: Re:AMBER: "personality" of Amber force field

From: Hui-Hsu Tsai (tsaih_at_ncifcrf.gov)
Date: Fri Mar 18 2005 - 15:22:11 CST

Thanks. Yes, I read this paper before. It talked about ff94 and ff99.
Does any one have experience or comment on the "personality" of ff02 and
ff03? My test so far shows they are also strongly helix-prone.
I do not have too much experience on Amber force fields.
Could amber expert or experienced users give me some comments?

Gavin

On Fri, 18 Mar 2005, Asim Okur wrote:

> Hi,
>
> Your observation about the parm99 force field has been reported couple
> of years ago. For more information please refer to ...
>
> Okur A, Strockbine B, Hornak V, Simmerling C
> Using PC clusters to evaluate the transferability of molecular mechanics
> force fields for proteins
> <http://wos02.isiknowledge.com/?SID=836GcD5p@@1BlLM9am6&Func=Abstract&doc=3/19>
> JOURNAL OF COMPUTATIONAL CHEMISTRY 24 (1): 21-31 JAN 15 2003
>
> Cheers,
>
> Asim Okur
>
>
> -------- Original Message --------
> Subject: AMBER: "personality" of Amber force field
> Date: Wed, 16 Mar 2005 11:01:00 -0500 (EST)
> From: Hui-Hsu Tsai <tsaih_at_ncifcrf.gov>
> Reply-To: amber_at_scripps.edu
> To: amber_at_scripps.edu
>
>
>
> Dear Amber community,
>
> I am writing this email to ask your comments on the "personality" of
> different amber force fields and GB models.
>
> In my GB + amber99 FF simulations, I oberserved the peptides and
> proteins are strongly helix-prone. Does any one has experience on
> amber02 FF? Does amber02 FF work better for b-strand formation? which GB
> model works better? any comment is welcome!
> Thanks.
>
> Gavin
>
>

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