[gmx-users] calculation of pKa values

Eric Jakobsson jake at ncsa.uiuc.edu
Wed Nov 24 17:17:08 CET 2004

For our lab's best take on this issue, see Mashl and Jakobsson, Biophysical 
Journal 2004

At 09:53 AM 11/23/2004 +0100, you wrote:
>Peter Trodler wrote:
>>Dear gmx users,
>>there are several tools to calculate pKa values of residues of a protein 
>>(TITRA,MCCE,MEAD,PDB2PQR,WHATIF). I am thinking which of this tools i 
>>should use to protonate the residues by pKa value, because the results 
>>are different, especially in the active site of proteins, and I don't 
>>want to protonate by standard pKa values. It is not easy to compare the 
>>results with experimental data, especially the protonation of ASP and 
>>GLU. Has somebody already compared this tools and can recommend me which 
>>tool I should use ?
>All pKa prediction program has advantages and disadvantages as you probably
>guess. I actually do not have any experience with the programs you mention but
>I have been using a program specially designed to consider the 
>of titratable groups to predict their pKa. It has been parametrized on 236 
>(or so)
>proteins and has been shown to give results as accurate as PB and is much 
>much faster
>(it takes about 20 minutes to predict pKas for the entiere protein). It 
>has also been
>adapted for membrane proteins.
>You can contact E.L. Mehler (elm2020 at med.cornell.edu) to get the code and 
>I can help
>for any questions.
>   Xavier Periole - Ph.D.
>   Dept. of Biophysical Chemistry / MD Group   Univ. of Groningen
>   Nijenborgh 4
>   9747 AG Groningen
>   The Netherlands
>   Tel: +31-503634329
>   Fax: +31-503634800
>   email: x.periole at chem.rug.nl
>   web-page: http://md.chem.rug.nl/~periole
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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
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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