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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Received on Mon Dec 12 2016 - 03:00:03 PST
