On Thu, Aug 08, 2002, Cozmuta wrote:
>
> I looked into the amber e-mail archive if there is anything related to
> protonation of proteins according to a certain pH.
There is nothing in Amber that does this. You would need to run some
external program to estimate the pKa's of all of the side chains, and use
that to guide the assignment of amino-acid protonation states.
One possibility is Don Bashford's MEAD program (www.scripps.edu/bashford);
but there is a large literature on this, and many other methods as well.
None are (yet) entirely reliable. One alternative is just to assume that
the pKa values in the protein are the same as for isolated amino acids; of
course this assumption could be modified by any experimental evidence you
might have.
..dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Aug 08 2002 - 15:05:25 PDT
