AMBER Archive (2004)

Subject: AMBER: calculation of pKa values

From: Peter Trodler (peter.trodler_at_itb.uni-stuttgart.de)
Date: Mon Nov 22 2004 - 02:32:25 CST

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 ?

I appreciate any help.

Best regards,

Peter Trodler

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