On Fri, Dec 14, 2012 at 2:20 PM, Shashidhar Rao <shashidharr.gmail.com>wrote:
> I would like to know if it is possible to build a random conformation of a
> peptide in AMBER (tleap) instead of the extended linear chain which can be
> minimized and subjected to dynamics to generate arbitrary conformations.
>
No. tleap will only build from templates (resulting in, as you've seen,
linear chains when no existing coordinates exist). You will have to build
the structure in a random conformation some other way, then load the
resulting PDB into tleap.
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 Dec 14 2012 - 12:30:02 PST
