On Fri, Nov 16, 2012 at 12:25 PM, Baptiste Legrand <bap.legrand.gmail.com>wrote:
> Dear all,
>
> I'm searching a protocol/tutorial to explore the torsion angles that can
> adopt a non-natural residue with amber (I'm not a specialist of these
> kind of calculations). Is there a particular routine to rotate step by
> step the phi and psi angles and to design an energy map? Thanks.
>
I wrote a script awhile back to do a single-torsion scan and extract an
energy map. If you see what this script is doing, it would be fairly
straightforward to extend this to a coupled-torsion surface like the
Ramachandran surface you're looking for.
At the very least, it'll give you an idea of how to scan a surface.
I sent the script to the mailing list awhile ago -- here is the relevant
thread where you can download the file:
http://archive.ambermd.org/201002/0249.html
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Nov 16 2012 - 11:30:03 PST
