Hi,
This is unrelated to the topic under which it was sent as a reply. If you
have a separate question, you should send a new email to
amber.ambermd.orgto avoid confusion make future searches for this
topic easier. But now onto
my answer...
My understanding of how proline is stitched into a protein sequence (this
generates extended poly-amino acid chains, not folded or even
partially-folded structures): There is a template (see
$AMBERHOME/dat/leap/lib) that provides the cartesian coordinates of each
atom along with the bonding information. When added into a sequence, the
proline coordinates are shifted to the end of the chain, and the HEAD of the
proline is bonded to the TAIL of the previous residue such that the bond
length is at its equilibrium value. However, the conformation/position of
the sidechain of every residue is completely specified by its conformation
in the template files. Simple rotations/translations will certainly modify
the cartesian coordinates, but the internal coordinates should be the same.
The leap source code contains what actually happens.
On Fri, Oct 29, 2010 at 11:42 AM, tanya singh <tanyabioinfo.gmail.com>wrote:
> Hi ,
>
> I need some help on proteins. I am developing a program to stitch amino
> acids templates and generate a linear polypeptide chain. The program is
> similar to the sequence command in amber.
>
> I am facing a problem in stitching the proline molecule becoz of the cyclic
> structure. Can you help me in figuring out a way to solve the proline
> problem.
>
> How does amber stitch proline so efficiently??
>
> thanks in advance
>
> Tanya Singh
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Oct 29 2010 - 11:00:04 PDT
