AMBER Archive (2009)

Subject: Re: [AMBER] Amber99SB

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Aug 11 2009 - 09:42:44 CDT

if you are using the Amber software, there will be no problem. there were
multiple errors in that study, including an incorrect conversion of the
ff99SB parameters for use in another program.
 You can also see the recent article
Evaluating the Performance of the ff99SB Force Field Based on NMR
Scalar Coupling Data*
*Lauren Wickstrom, Asim Okur, Carlos SimmerlingBiophysical Journal, *Volume
97, Issue 3*<http://www.cell.com/biophysj/issue?pii=S0006-3495%2809%29X0016-0>,
853-856, 5 August 2009

doi:10.1016/j.bpj.2009.04.063

On Tue, Aug 11, 2009 at 10:33 AM, eric johnson
<eric_m_johnson_at_hotmail.com>wrote:

>
> Several force fields, including Amber99SB, were used to calculate NMR
> scalar couplings in the following study:
> Best, R.B. et al. 2008. Are current molecular dynamics force fields too
> helical? Biophys. J. 95:L7-L9.
> A correction was later reported that indicates that Amber99SB was not
> implemented correctly in this study.
> Best, R.B. et al. 2008. Biophys. J. 95:4494.
> I use the Amber99SB force field and want to avoid any likely missteps. Is
> there a common pitfall?
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