AMBER Archive (2009)

Subject: Re: [AMBER] only ff94 and ff99 for GBSA?

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Mon Jul 27 2009 - 11:41:27 CDT

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?

Best regards,
Andrew

03.06.09, 16:24, "David A. Case" <case_at_biomaps.rutgers.edu>:

> On Wed, Jun 03, 2009, Andrew Voronkov wrote:
> > By the way, the template protein has 1,35 angstroms X-ray structure
> > resolution. So, first of all I want to look which RMSD I'll get for
> > the template protein by use of the implicit solvent - if it would be
> > much more than 1.35 A then I want to switch the implicit solvent to the
> > explicit one. I've done already such simulations with igb=2 and gbsa=1
> > for amber03 for template protein during 2 ns and average RMSD was about
> > 2,5-3 angstroms (with some serious local structure changes) against
> > 1,3-1,4 angstroms RMSD with TIP3P octahedral 8 angstrom box during 2 ns
> > run. Maybe I need to switch amber03 to amber99 or amber94 to get better
> > RMSD with implicit solvent.
> It's not uncommon for GB simulations to move further from a crystal structure
> than explicit solvent calculations do. Some of this may be because motions
> are much faster in the absence of friction, but some is almost certainly due
> to limitations of the Amber GB models, and/or the ff03 force field.
> > In Amber 10 user's guide, p.51 is written: "The Generalized Born/Surface
> > Area Model can be used instead of explicit water for non-polarizable
> > force fields such as ff94 and ff99" - that's why I have such a question.
> This will be fixed in the next release. See Chapter 2 of the AmberTools
> manual for information about force fields. As Carlos suggested, please don't
> use ff94 or ff99 -- these are not even available in the current release unless
> you specifically ask for an "old" force field.
> ...dac
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