AMBER Archive (2009)
Subject: Re: [AMBER] only ff94 and ff99 for GBSA?
From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jun 03 2009 - 07:24:56 CDT
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.
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