Hi,
In addition to what Josh said, you could take a look at these relevant
papers which use Amber to stretch DNA:
Roe, D.R. and Chaka, A.M., Structural Basis of Pathway-Dependent Force
Profiles in Stretched DNA J. Phys. Chem. B, 2009, 113 (46), pp 15364–15371
http://pubs.acs.org/doi/abs/10.1021/jp906749j
Piana, S., Structure and energy of a DNA dodecamer under tensile load *NAR*,
*2005*, 33, p.7029-7038.
http://nar.oxfordjournals.org/content/33/22/7029
-Christina
On Tue, Dec 8, 2015 at 3:12 AM, Josh Berryman <
the.real.josh.berryman.gmail.com> wrote:
> Hello Jack,
>
> the forcefield file is not what you are after.
>
> The section or the manual on NMR restraints should give you instructions
> for setting up a positional restraint, these are commonly used for
> pulling-type simulations. AFAIK for moving restraints, the normal
> procedure is just to retart the simulation every few nanoseconds with the
> restraint minimum at a new position, by defining a relatively soft
> potential and by making only small jumps then you can avoid jagged lines in
> your output data.
>
> Josh
>
>
>
>
> On 7 December 2015 at 18:29, Jack Shepherd <jws526.york.ac.uk> wrote:
>
> > Hi all,
> >
> > I am interested in applying external forces to a length of DNA (eg at the
> > terminal base pairs to stretch the molecule), but not exactly sure about
> > it. Is it simply a case of suitably editing the forcefield file, or is
> > there more to consider?
> >
> > Thank you in advance
> > Jack Shepherd
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652 / Fax: (801) 585-6208
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Received on Tue Dec 08 2015 - 07:30:04 PST
