AMBER Archive (2009)

Subject: RE: [AMBER] Can I do DNA bending with AMBER?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon Aug 17 2009 - 01:00:08 CDT

Thank you Prof. Case.

 

Cat
 
> Date: Sun, 16 Aug 2009 09:13:05 -0400
> From: case_at_biomaps.rutgers.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] Can I do DNA bending with AMBER?
>
> On Sun, Aug 16, 2009, Catein Catherine wrote:
> >
> > I am trying to study the DNA bending due to DNA modifications. I wonder
> > if it is typically feasible to do the calculations with AMBER. Are
> > there any precaution should I take into account?
>
> There have been lots of studies of DNA bending with un-modified DNA. Study
> these and see if they seem feasible to carry out with modifications. Think
> about how accurate and precise a result you would need to obtain to really see
> the effect of the modification. And make sure that you have a good chance of
> learning something new -- your goal should not be to just reproduce some value
> that has already been measured.
>
> ...dac
>
>
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