AMBER Archive (2009)

Subject: Re: [AMBER] ask for parm99MOD

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu May 28 2009 - 16:52:29 CDT

On Thu, May 28, 2009, Carlos Simmerling wrote:

> unless you have a reason to think about ff02, don't involve it any more.

Just my two cents here: Unless you are explicitly trying to reproduce some
old result, we advise that people only use force fields in
$AMBERHOME/dat/leap/cmd, and *not* those in the "oldff" subdirectory, which
are only there for historical completeness.

The ff02 model has undergone some amount of torsional reparameterization, as
discussed in Wang et al, (2006) JCC, 27(6), 781-790. However, this is a
polarizable force field, and hence is not compatible with any of Amber GB
models. You could use leaprc.ff02pol.r1 ("r1" = revision 1) for explicit
solvent simulations, but not for GB.

> if you just want to run the best simulation that you can, I suggest ff99SB
> (but be careful with GB, the GB-OBC model is very good but does have a few
> minor weaknesses that have also been reported in the literature).

Just to expand, be sure to read this paper:

%A D.R. Roe
%A A. Okur
%A L. Wickstrom
%A V. Hornak
%A C. Simmerling
%T Secondary Structure Bias in Generalized Born Solvent Models: Comparison of
Conformational Ensembles and Free Energy of Solvent Polarization from Explicit
and Implicit Solvation
%J J. Phys. Chem. B
%V 111
%P 1846-1857
%D 2007

(Carlos can chime in if there are others as well).

...dac

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