[gmx-users] About pKa calculations and dipoles

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 12 22:01:07 CET 2002

On Tue, 12 Mar 2002, Markus O Kaukonen wrote:

>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)
It depends. 

>If so, please give relevant (and hopefully review type) references.
Check out work by Don Bashford (www.scripps.edu/bashford)

>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.
Point charges have the same effect: SPC water has a permanent dipole of
2.3 D.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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