Re: AMBER: Harmonic constraints

From: Carlos Simmerling <>
Date: Mon, 10 Sep 2007 10:14:54 -0400

are we allowed to distrib a parmbsc0 parm.dat file on the amber web site?

On 9/7/07, Thomas Cheatham <> wrote:
> > Hi Ilyas,
> > I mean that ff99 for proteins has completely wrong behavior for
> > Gly as well as much too strong helical content for other residues.
> > ff99SB has (mostly) corrected these. Since so many papers have
> > pointed out trouble with ff99 for proteins, I would expect good
> reviewers
> > to be unwilling to accept any new work done using these parameters.
> I wouldn't be quite so extreme here as we all know that all classical
> treatments and force fields have limitations... The key is whether you
> can assess and validate your simulation results and if you can explain
> and/or reproduce experiment with a given force field. Clearly the ff99sb
> force field, in my experience, behaves better for proteins and Prof.
> Simmerling points out serious limitations with ff94 and ff99 (glycine and
> also overstable alpha helices as discussed in detail in their proteins
> article); in addition to ff99sb, the ff03 seems to behave better than ff99
> in my experience.
> However I really reply since I know Ilyas likes nucleic acids and his
> comment probably relates to the question of performance of ff99 in the
> context of nucleic acids; there, with all of the parm9X force fields there
> are subtle biases in the DNA backbone leading to anomalous (alpha, gamma)
> = g+, t states. For nucleic acids, people may be better off with the
> parmbsc0 force field (see Orozco and co-workers, Biophys J. 2007, ~July).
> Moreover, there are subtle artifacts with salt parameters (see the
> Auffinger article JCTC ASAP).
> Finally, if force field artifacts or limitations are known, it becomes
> incumbant on the user or paper author to acknowledge those limitations,
> note how they may influence their results, and convince the reviewers or
> readers that these artifacts do not unduly influence the results. This
> gets back to the assessment and validation of the results; we can model
> anything, but do we actually model reality and/or explain experiment?
> -- tec3
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Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
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Received on Wed Sep 12 2007 - 06:07:27 PDT
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