AMBER Archive (2002)

Subject: Re: protonation pH dependent

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 08 2002 - 17:05:25 CDT

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 

-- 

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