Hello James,
There is really a lot of room for discussion regarding your questions.
Considering peptide conformations is complicated business and there is
generally not "a" structure. There is great conformational flexibility
even for small, constrained, cyclic peptides. As for the MD - yes, a
classical MD trajectory is entirely determined by the starting
structure. One can introduce random number seeds, high temperature, etc
... to explore greater space, but where you start is definitely worthy
of thoughtful consideration.
I can send references and more discussion off list, if you are
interested.
Cheers,
Jim N.
________________________________________________________
James Nettles, Ph. D. Computational Pharmacology
Liotta/Snyder Group, Modeling Division, Department of Chemistry
Emory University 1515 Pierce Dr. Atlanta, Ga. 30322
jnet...@emory.edu TEL: (404)966-4617 FAX: (404)728-0991
________________________________________________________
On Aug 15, 2005, at 11:36 AM, James R. Graham wrote:
Hello All,
How "physiological" are the structures that are produced from builder?
Meaning, how are the angles, etc. determined? Might such a resulting
structure mimic a chemically-synthesized peptide?
I have taken peptides I created using builder and done some MD
simulations and the structures certainly change, but I wonder whether
the changes are limited by the initial starting structure...which is,
of course, a question for another mailing list, I suppose. ;)
james
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