I need to build a cyclic peptide as the initial conformation for
further simulations, not only for displaying purposes.
I will try what you say and I will see.
Thank you.
-- Moshe Goldstein
Quoting Tsjerk Wassenaar <tsje...@gmail.com>:
Hi Moshe,
No it isn't. PyMOL is a molecular viewer/graphics engine, not a
modeling package. However, it's not too hard to do using your
favourite MD package. With the definition of a bond and some energy
minimization you'd get close. If it's for displaying purposes only,
that might even be enough.
Cheers,
Tsjerk
On Fri, Feb 15, 2008 at 1:17 AM, <goldm...@fh.huji.ac.il> wrote:
Hello.
I am new to PyMOL.
Very easily I succeeded to build a linear peptide, given its sequence.
I want to build a cyclic peptide for the same sequence, connecting the
C-terminus with the N-terminus. I know that the bond that is created
that way is too long - it should be, also, some
(automatic/algorithmic) way to rearrange the cyclic structure in order
to have an acceptable bond length.
Is this possible to do with PyMOL?
Thanks for your help.
-- Moshe Goldstein
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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