RE: AMBER: Harmonic constraints

From: Hu, Shaowen (JSC-SK)[USRA] <"Hu,>
Date: Mon, 10 Sep 2007 09:05:18 -0500

For a system of protein-DNA complex, is it possible to apply parm99sb to
the protein but parmbsc0 to the nucleic acid?


-----Original Message-----
From: on behalf of Jiri Sponer
Sent: Sat 9/8/2007 1:07 AM
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 <> 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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Received on Wed Sep 12 2007 - 06:07:26 PDT
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