On Wed, Apr 2, 2014 at 9:33 AM, Urszula Uciechowska <
urszula.uciechowska.biotech.ug.edu.pl> wrote:
> Dear Amber users,
>
> I am trying to apply distance constraints between the residue of my
> portein and nuc.acid of my DNA molecule. Can someone suggest me how should
> I start.
> I went through the Tutorial 4 but do not know how to relate it to my case.
> Sould I prepare 7colum file?
> Could anyone suggest me something?
>
See chapter 6 of the Amber 12 manual (regarding NMR restraints). It
describes how to set up geometric restraints in your system (AFAIK, there's
no way to impose geometric constraints outside of SHAKE, but hopefully you
can accomplish what you want with the harmonic restraints instead).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Apr 02 2014 - 07:00:07 PDT
