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

From: Viktor Hornak <>
Date: Wed, 01 Mar 2006 16:16:13 -0500

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

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.


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Received on Sun Mar 05 2006 - 06:10:13 PST
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