[gmx-users] About pKa calculations and dipoles

Markus O Kaukonen mokaukon at cc.helsinki.fi
Tue Mar 12 12:00:19 CET 2002

Dear All,

Can one accurately enought calculate free energies of the
proteins in polar solutions (or for membrane proteins exposed  partly to
lipids and partly to water) in order to get reasonable pKa or pKa_int
(pKa == pH at which half of the group in question (usually an aminoacid)
have the proton, pKa_int == the same as above except keeping all other
ionizable groups neutral)

If so, please give relevant (and hopefully review type) references.

I got the impression that including the protein permanent dipoles, induced
dipoles and water dipoles are extremely important (in addition to direct
coulomb terms in the total energy) when calculating the changes in free
energies in proteins ( by reading an excellent but old review
[A. Warshel and S. T. Russell, Quaterly Review of Biophysics
 17, 3 (1984) pp. 283-422] ). The dipole contributions
(permanent, induced and water) seem  often to
account for about 50% of the free energy changes
(and thus of solvation energies, and pKa values).

To me it seems that Gromacs has point charges and perhaps induced dipoles
there (Gromacs pdf manual, Sec. 3.5 )
but missing permanent dipoles in proteins and water.

If one does not have the crucial bits in the total energy (permanent and
water dipoles) how one can calculate any meaningfull results?

Hope I got this totally wrong. Please correct me.

Cheers, Markus

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