AMBER Archive (2007)

Subject: Re: AMBER: MD_model

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Dec 05 2007 - 17:54:50 CST

Apart Thomas's explanation, I wanted to add something about fixing the
backbone. There are a couple of ways to do this. In one of my systems, I
have used the positional restrains to keep the structure close to the
initial structure. What this means is that you will sample around the
initial structure in the phase. You can also use torsional NMR restraints
to keep the backbone close around a particular conformation. I would
suggest to use the positional restraints because it is very easy. Good
luck.

On Thu, 6 Dec 2007, Urszula Uciechowska wrote:

>
> Dear Amber users,
>
> I have a protein model and I would like to simulate it for about 400 ps at 300K keeping the
> backbone fixed.
> Could someone maybe give me some example o such a input file?
> thank you in advance
>
> Best Regards,
> Urszula Uciechowska
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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