AMBER Archive (2009)

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

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Wed Jun 03 2009 - 06:52:13 CDT

"AMBER Mailing List" <amber_at_ambermd.org>
03.06.09, 14:51, "Carlos Simmerling" <carlos.simmerling_at_gmail.com>:
> ff03 slightly favors alpha helix compared to ff99SB. since igb=5 favors
> helix, I would not use them together. igb=7 seems to weaken most secondary
> structure overall and in my opinion needs some refitting before extensive
> production use.
> the "best" combination depends on what you plan to do- is it for protein MD,
> or just MM-GBSA postprocessing?

It is for protein MD. I want to look over the stability of the structures. I have several homology based models which I want to refine by MD simulations - to get average minimized structures from last parts of the trajectories.
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.

> do NOT use ff94 or ff99 with GB, you will get only helix!
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.

> On Wed, Jun 3, 2009 at 6:28 AM, Andrew Voronkov <drugdesign_at_yandex.ru>wrote:
> > Dear amber users,
> > as far as the amber03 force field was parametrized with usage of
> > electrostatic continuum models then it must be used with some correction
> > parameters or not to be used at all with implicit solvent, right? I want to
> > use amber03 with GBSA (igb=2 or 5 or 7) method and set up dielectric
> > constant to 4 for the protein as was used in amber03 parametrization. Is it
> > enough for usage of ff03 or it is better to use ff99 or ff94 with GBSA?
> >
> > Best regards,
> > Andrew
> >
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