This directory contains the data and parameter files needed to
reproduce some of the results reported in D. Bashford & K. Gerwert
"Electrostatic Calculations of the pKa Values of Ionizable groups in
Bacteriorhodopsin" J. Mol. Biol. vol. 224 pp. 473-486 (1992).

To do the electrostatic calculations for the Henderson structure (HE)
run the commands,

   ../multiflex -epsave_oldway -blab1 -epsin 4.0 -membz -23.8 21.2 -membhole 10.0 HE > HE.big.output.file

This will take about eight hours on a SparcStation 2, or 45 minutes on
a Cray Y-MP.  The intrisic pK's and the site-site couplings will be
written to HE.pkint and HE.g, repectively.  Details on self energy,
background contribution and so on can be found in the big output file.
Leaving out the "-epsave_oldway" flag will increase the accuracy of
the Poisson-Boltzmann solver and give .pkint and .g file results that
differ from the paper by a few tenths of a pK unit.  Edit the
resulting HE.pkint file to change the intrinsic pK for the Schiff base
( LYR-216) to 40.0.  The paper explains why we do this.

To do the titration curves, run

   redti HE

This takes only a few minutes.  The pKhalfs will be in HE.pkout
The resulting HE.pkout file should match the "HE" results of our
paper.  If you omitted the "-epsave_oldway" flag from the multiflex
run, you may get substantial differences because small changes in
pkint and site-site coupling values can lead to larger changes in
calculated pKhalf values.  This sensitivity is discussed in
our papers on bacteriorhodopsin and myoglobin.

To do the same calculations for the "arginine up" structure (RU)
repeat the above with HE --> RU, except that the Schiff base pKint
should be set by hand to -0.8.

NOTE:  The calculated pkint for LYR-216 may not come out the same
as what we report in the paper.  This is caused by the fact that
the LYR model compound is so large that part of it falls outside
of the finest grid box (61 points per side, 0.25 Ang spacing).
Something more like the result in the paper can be obtained by using
a 81 points per side, but the distinction is unimportant since we
must set the LYR pkint by hand anyway.

