AMBER Archive (2006)

Subject: Re: AMBER: failed to save prm and xyz using ff96

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Wed Mar 01 2006 - 15:16:13 CST

Joseph Nachman wrote:

>Can yuo recommend any of the papers discussing the problems of parm96?
>
>
>>I would also add my opinion that unless you have a very good reason,
>>you should not be using parm96. It has some serious problems
>>that have been documented in the literature.
>>
>>

Here is a few papers dealing with ff96 (I am sure there's more), in
particular check Ono et al that specifically discusses the propensity of
ff96 to form extended structures:

Kamiya N, Higo J, Nakamura H. Conformational transition states of a
beta-hairpin peptide between the ordered and disordered conformations in
explicit water. Protein Science 2002;11(10):2297-2307.

Higo J, Ito N, Kuroda M, Ono S, Nakajima N, Nakamura H. Energy landscape
of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn,
beta-hairpin, and other disordered conformations. Protein Science
2001;10(6):1160-1171.

Ono S, Nakajima N, Higo J, Nakamura H. Peptide free-energy profile is
strongly dependent on the force field: Comparison of C96 and AMBER95. J
Comput Chem 2000;21(9):748-762.

Wang L, Duan Y, Shortle R, Imperiali B, Kollman PA. Study of the
stability and unfolding mechanism of BBA1 by molecular dynamics
simulations at different temperatures. Protein Science 1999;8(6):1292-1304.

Cheers,
-Viktor

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu