[gmx-users] Including pH in Your run...

Eric Jakobsson jake at ncsa.uiuc.edu
Mon Feb 2 07:21:02 CET 2004

A student in my lab, Sameer Varma, has just published on the problem of 
computing ionization states in situations where multiple titratable 
residues interact electrostatically with each other.  It is at

Sameer Varma and Eric Jakobsson
Ionization States of Residues in OmpF and Mutants: Effects of Dielectric 
Constant and Interactions between Residues
Biophys. J. 2004 86: 690-704. [Abstract] [Full Text]


At 06:47 PM 1/31/2004 +0100, you wrote:
>Hi Gromacs Community...!
>I've been working on an additional module for Gromacs which will be able 
>to add protons to your
>periodic box and predict effects of protonation on protein (depending on 
>Ka of amino acids) - calculate
>pI of polipeptide (I have to discuss my method with other people from my 
>University  ) .
>I'll relase the beta version of this module at the very beginning  of the 
>March... I hope it will work properly.
>Best regards !!!
>Kamil Tamiola
>Univeristy of Wroclaw

Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

(Currently on leave to NIH to serve as Director of Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medical Sciences and Chair of the NIH Biomedical Information 
Science and Technology Initiative Consortium.  Usual schedule is four days 
a week at NIH and three days a week at Illlinois.)

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