[gmx-users] calculation of pKa values

Xavier Periole x.periole at chem.rug.nl
Tue Nov 23 09:53:42 CET 2004

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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