AMBER Archive (2009)
Subject: Re: [AMBER] only ff94 and ff99 for GBSA?
From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Tue Jul 28 2009 - 01:12:15 CDT
Amber ff99SB field still has the same partial scheme from Amber99, right? And this partial charges scheme is different from amber03, so I'm a bit confused about choice of the force field for proteins molecular dynamics.
27.07.09, 21:05, "case" <case_at_biomaps.rutgers.edu>:
> On Mon, Jul 27, 2009, Andrew Voronkov wrote:
> > Dear Dr Case, what you can say about AMBER99SB force field? Is it also
> > considered as an "old" force field? It has several parametrization
> > improvements toward the Amber99 force field?
> No. ff99SB is quite "up to date". If you look in amber10/dat/leap/cmd, you
> will see the force fields we currently are recommending for most simulations.
> Older force fields are in the "oldff" subdirectory -- they are preserved so
> that old results can be checked, are differences investigated. Material in
> the "oldff" directory are not generally recommended for new simulations.
> Of course, there is some subjectivity here, and the opinions of the Amber
> devleopers are not definitive. This is still research.
> ...hope this helps...dac
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