AMBER Archive (2007)

Subject: Re: AMBER: Harmonic constraints

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 10 2007 - 09:14:27 CDT

yes it is, you can take the parmsbc0 file and change the phi/psi parameters
to match parm99sb. we'll put such a file on the amber web page soon.

On 9/10/07, Hu, Shaowen (JSC-SK)[USRA] <Shaowen.Hu-1_at_nasa.gov> wrote:
>
>
> For a system of protein-DNA complex, is it possible to apply parm99sb to
> the protein but parmbsc0 to the nucleic acid?
>
> Thanks,
> Shaowen
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu on behalf of Jiri Sponer
> Sent: Sat 9/8/2007 1:07 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Harmonic constraints
>
> Just a short comment.
> For DNA, them problems of parm94/99 are so substantial that parmbsc0
> (Perez....Orozco BJ 2007) should be applied, to my opinion, immediately.
> The first a/g flips may occur as early as in equilibration, making, for
> example, the subsequent analysis of local conformational variations in
> B-DNA substantially biased.
>
> For RNA, the a/g problem basically does not occur (flips are reversible)
> and so far we detected only minor differences!
> So we use both parmbsc0 and parm99 to see eventual differences as RNA
> backbone has numerous conformational classes.
>
> I obviously cannot comment on proteins, but we switched entirely to the
> new force field parm99sb.
>
> Best wishes, Jiri
>
>
> [ Charset ISO-8859-1 unsupported, converting... ]
> > I completely agree with Tom - I had just meant that for the kind of
> > simulations most people are doing, IMO the community should no longer
> > accept ff99-based data (for proteins) without extremely compelling
> > evidence that the results are reliable. Of course there are many kinds
>
> > of simulations that may be ok with ff99 (such as very short or
> > completely restrained runs), and I don't mean to imply that old data
> > with ff99 was always wrong.
> > My point is just that we know there are serious limitations and there
> > are better options available that do not increase simulation
> > complexity, so we as a community should expect new research to either
> > use the better models or else explain why it was not done.
> > It's not unlike using a distance-dependent dielectric treatment for
> > water- it might still be useful in some cases, but generally I think
> > we all place higher demands for validation of that kind of data than
> > we might with a "better" treatment of solvation. Ideally all
> > simulations should be validated against experiment, but we should be
> > more suspicious of data generated using models that have serious and
> > well-documented weaknesses.
> >
> > I'm stressing this point because I find many people remain unaware of
> > the improvements in force fields over the past years and still begin
> > new projects with old/poor parameters. Of course ongoing projects may
> > require old parameters for consistency, but one should be aware of the
>
> > limitations (and as Tom says, address them accordingly in
> > publications). Unfortunately not all reviewers are requiring this.
> > carlos
> >
> > On 9/7/07, Thomas Cheatham <tec3_at_utah.edu> wrote:
> > >
> > >
> > >
> > > Finally, if force field artifacts or limitations are known, it
> > > becomes incumbant on the user or paper author to acknowledge those
> > > limitations, note how they may influence their results, and convince
>
> > > the reviewers or readers that these artifacts do not unduly
> > > influence the results. This gets back to the assessment and
> > > validation of the results; we can model anything, but do we actually
> model reality and/or explain experiment?
> > >
> > > -- tec3
> > >
> > >
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