Re: [AMBER] How to determine the protonation state of phosphorylated residue in a protein?

From: Jason Swails <>
Date: Sun, 22 Apr 2012 18:31:10 -0400

I would first look to see if it's mentioned in the literature (specifically
in experimental papers). If the pKa is not known (even roughly)
experimentally, then there are a couple software options:

I've heard of propka and H++, but I've never used either one (and I'm not
positive that either will work with a phosphorylated amino acid, but you
can try).



On Thu, Apr 19, 2012 at 8:08 PM, Rajendra Sharma <>wrote:

> Dear all,
> I have been working on a histidine kinase from E.coli. I need to add a
> phosphate to the histidine. However, I not not sure how to determine the
> protonation state of this modified histidine residue in the protein. Could
> anyone suggest for programs to do it?
> Sincerely,
> Rajendras
> --
> Rajendra Sharma
> Junior Research Fellow,
> Computational Biophysics,
> *National Center for Biological Sciences,*
> (Tata institute of Fundamental Research)
> India.
> Mobile No. +91-9950675288
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sun Apr 22 2012 - 16:00:02 PDT
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