AMBER Archive (2009)
Subject: Re: [AMBER] ask for parm99MOD
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jun 01 2009 - 15:12:47 CDT
sorry for the slow follow-up. here's another reference from my group. there
are certainly many other papers that are relevant, so make sure to check out
some of the ones we cite as well
**Okur, A., Wickstrom, L. and Simmerling, C.,* “Evaluation of salt bridge
structure and energetics in peptides using explicit, implicit and hybrid
solvation models”*, J. Chem. Theory Comput., 4:288-298 (2008)
On Thu, May 28, 2009 at 5:52 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:
> 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,
> 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
> > (but be careful with GB, the GB-OBC model is very good but does have a
> > 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
> Conformational Ensembles and Free Energy of Solvent Polarization from
> 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).
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