AMBER Archive (2009)

Subject: RE: [AMBER] ask for parm99MOD

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Mon Jun 01 2009 - 15:25:02 CDT

thanks, I am reading a lot of papers on force fields from Giants like you and others. Later on, I think I will have a rough idea of how to choose an appropriate force field in Amber for my studying system.

> From: carlos.simmerling_at_gmail.com
> Date: Mon, 1 Jun 2009 16:12:47 -0400
> Subject: Re: [AMBER] ask for parm99MOD
> To: amber_at_ambermd.org
>
> 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,
> > 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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> >
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