AMBER Archive (2007)

Subject: Re: AMBER: Harmonic constraints

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Sep 07 2007 - 13:52:48 CDT

> 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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