AMBER Archive (2005)

Subject: Re: AMBER: conformational sampling of a peptide

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Tue May 24 2005 - 10:26:52 CDT

Hello hannes -

As a quick and dirty way, try using: slow-cool simulated annealing in
vacuo: het yuor system up to 2000-3000K, generate a high number (say, 50
or more) of random random structures, then slowly cool down each one.

Good luck,

Joseph

On Tue, 24 May 2005, Hannes Barsch wrote:

> Dear AMBER community,
>
> I work on the conformational sampling of a dye labelled oligo peptide. The
> peptide is 9 amino acids in length, of which 8 are frozen using IBELLY. The
> last amino acid and the dye bonded to the first aa are to move freely to
> investigate the distance distribution over time. Energies are of no
> interest - the sampling is just a coarse study.
> After having run ordinary MD simulations I found out that the dye is stuck
> in an energetic minimum and hardly moves. Therefore, I have changed the
> force field parameters of the atoms linking dye and peptide: all torsional
> potentials were set to zero as well as the bond angle potentials.
> Electrostatics were switched off by raising DIELC to 1000000 in the sander
> MD input file.
> Still the movement of the dye moiety has not improved very much. It still
> sticks to the peptide backbone. I guess this might be due to the nonbounded
> interaction. How can I switch these interactions off? I already tried to
> reduce CUT in the sander input file but I can do so only down to just above
> 8.0 A. Is there a better or may be an easier way to work with a pseudo hard
> sphere model in AMBER?
> Thanks for any hints!
> Regards,
>
> Hannes
>
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Joseph Nachman				Department of Biochemistry
nachman_at_hera.med.utoronto.ca		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
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