Hi,
Dan Roe has done some DNA stretching/pulling simulations using AMBER:
http://pubs.acs.org/doi/abs/10.1021/jp906749j
On Mon, Dec 12, 2016 at 5:41 AM, Josh Berryman <
the.real.josh.berryman.gmail.com> wrote:
> Sarah Harris has done some DNA pulling simulations with amber eg here
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305225/
>
> In general I think you have to start and stop the simulations with new
> restraint positions every 100ps or so (depending on restraint strength),
> and try to make sure that you don't move the restraints too far too
> suddenly.
>
> I'm trying to pull DNA myself at the moment, I've just sent a bug report to
> devlist that restraints aren't working with the bleeding-edge versions of
> pmemd.cuda.
>
> Josh Berryman
>
>
>
> On 12 December 2016 at 03:31, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > Not that I know of, and I looked into it for this by the way:
> >
> > http://phobrain.com/pr/home/mol.html
> >
> > Bill
> >
> > On 12/11/16 6:15 PM, The Cromicus Productions wrote:
> > > I was thinking on fixing the first and last base pairs and using an
> > > external force in order to make the helix become a stair. Is it
> possible
> > to
> > > define external forces?
> > >
> > > On Sun, Dec 11, 2016 at 9:12 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > >
> > >> E.g. high temperature is pretty easy to accomplish.
> > >>
> > >> Bill
> > >>
> > >>
> > >> On 12/11/16 6:05 PM, David A Case wrote:
> > >>> On Sun, Dec 11, 2016, The Cromicus Productions wrote:
> > >>>> I want to simulate the untwisting of a DNA molecule. Is this
> possible
> > >> with
> > >>>> AMBER?
> > >>> You would have to decide what physical or artifical forces were
> driving
> > >> the
> > >>> untwisting. The model those forces.
> > >>>
> > >>> ....dac
> > >>>
> > >>>
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--
---------------------------------------------------------------------------------------
Christina Bergonzo
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
http://home.chpc.utah.edu/~cheatham/
---------------------------------------------------------------------------------------
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Received on Mon Dec 12 2016 - 05:00:02 PST
