Re: AMBER: "personality" of Amber force field

From: Hui-Hsu Tsai <tsaih.ncifcrf.gov>
Date: Fri, 18 Mar 2005 18:05:07 -0500 (EST)

I tried beta-hairpin using amber ff99 + GB model. It forms helix quickly
in conventional MD simulation at 325 K. I do not have this experience to
observe helix formation so fast in CHARMM FF. Maybe I should use replica
exchange MD to generate the decoy to examine the population of
helix and beta secondary structures.

Gavin


On Fri, 18 Mar 2005, Adrian E. Roitberg wrote:

>
> HI,
> It would be useful to give us more details on the meaning of 'helix prone'.
>
> What system is this ? who do you know it is not a helix all the way ?
>
> Thanks
>
> Hui-Hsu Tsai wrote:
> > Thanks. Yes, I read this paper before. It talked about ff94 and ff99.
> > Does any one have experience or comment on the "personality" of ff02 and
> > ff03? My test so far shows they are also strongly helix-prone.
> > I do not have too much experience on Amber force fields.
> > Could amber expert or experienced users give me some comments?
> >
> > Gavin
> >
> >
> > On Fri, 18 Mar 2005, Asim Okur wrote:
> >
> >
> >>Hi,
> >>
> >>Your observation about the parm99 force field has been reported couple
> >>of years ago. For more information please refer to ...
> >>
> >>Okur A, Strockbine B, Hornak V, Simmerling C
> >>Using PC clusters to evaluate the transferability of molecular mechanics
> >>force fields for proteins
> >><http://wos02.isiknowledge.com/?SID=836GcD5p.@1BlLM9am6&Func=Abstract&doc=3/19>
> >>JOURNAL OF COMPUTATIONAL CHEMISTRY 24 (1): 21-31 JAN 15 2003
> >>
> >>Cheers,
> >>
> >>Asim Okur
> >>
> >>
> >>-------- Original Message --------
> >>Subject: AMBER: "personality" of Amber force field
> >>Date: Wed, 16 Mar 2005 11:01:00 -0500 (EST)
> >>From: Hui-Hsu Tsai <tsaih.ncifcrf.gov>
> >>Reply-To: amber.scripps.edu
> >>To: amber.scripps.edu
> >>
> >>
> >>
> >>Dear Amber community,
> >>
> >>I am writing this email to ask your comments on the "personality" of
> >>different amber force fields and GB models.
> >>
> >>In my GB + amber99 FF simulations, I oberserved the peptides and
> >>proteins are strongly helix-prone. Does any one has experience on
> >>amber02 FF? Does amber02 FF work better for b-strand formation? which GB
> >>model works better? any comment is welcome!
> >>Thanks.
> >>
> >>Gavin
> >>
> >>
> >
> >
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> >
>
>

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Received on Fri Mar 18 2005 - 23:53:00 PST
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