AMBER Archive (2007)

Subject: Re: AMBER: ab initio modeling using Amber

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Feb 01 2007 - 22:07:45 CST

Hi,

If you notice, in the article you mention the authors do not create
the structures with Amber. The structures were built with a number of
other programs, and the final set was just minimized using an Amber
*force field* (not the Amber program - the program used was actually
Tinker).

For this last step you could, of course, use the Amber program just as
well. However, to generate the structures, you should probably look
at the other programs they used, like RAPPER, SCWRL, RAMP and RAPDF.

HTH,
Gustavo.
P.S.: I should also point out that, mentioning just "Amber force
field" is actually incomplete, for the authors should also have
mentioned which specific parametrization of the Amber force field was
used (ff94, ff99, ff99SB, etc.). From the reference, I suppose it was
the ff94.

On 2/1/07, snoze pa <snoze.pa_at_gmail.com> wrote:
> Dear Amber Users,
> Is it possible to use amber for ab initio calculations. I want to model a
> small protein for which no PDB template available
> so I want to use ab initio technique. If yes, is there any tutorials
> available in AMBER. There is a paper published in Proteins,
> 2003 "Ab initio construction of polypeptide fragments: Accuracy of loop
> decoy discrimination by an all-atom statistical
> potential and the AMBER force field with the Generalized Born solvation
> model by de Bakker PI, DePristo MA, Burke DF,
> Blundell TL.Proteins. 2003 Apr 1;51(1):21-40.
> thank you
> snoze
>
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