You can using leap, but it will just be a long unfolded peptide. The
problem you are talking about (i.e. primary structure -> tertiary
structure) is a major unsolved problem in the field.
That being said, your best bet is probably to try and homology model it,
for which there are a vast number of applications out there (but none are
part of AMBER). If that fails, you can try an ab initio prediction, for
which there are fewer options (also none are part of AMBER).
So overall, unless you were hoping to simulate the folding up of your
protein (a very hard problem), you'll need to investigate options for
getting a good starting structure.
~Aron
On Thu, Nov 8, 2012 at 2:18 PM, Sindrila Dutta banik <
sindrila.duttabanik.yahoo.com> wrote:
> dear all
>
> I have primary sequence of a protein. Can I generate 3D structure of the
> same using xleap? Or any other software can do this?
>
> Please let me know.
>
> Sindrila
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Nov 08 2012 - 14:30:08 PST
