Hi Jason,
thanks for the clarification. I will do a detailed Google search to see
what is available for building random conformations of peptides. I came
across something called "CRANKITE" in the quick survey.
shashi
On Fri, Dec 14, 2012 at 2:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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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>
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Fri Dec 14 2012 - 12:30:03 PST
