AMBER Archive (2009)

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

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Aug 16 2009 - 08:13:05 CDT

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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber