calculation of pKa values

[Peter Trodler <peter.trodler*at*itb.uni-stuttgart.de>]

 Dear ccl 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 dont 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 ?
 I appreciate any help.
 Best regards,
 Peter Trodler