I am new to CHARMm and the poisson boltzmann calculation. I want to solve the
equation for a channel (with a pore) placed in a membrane. TO do this I place the
channel on a grid, all gridpoints outside the channel are assigned the dielectric of 80
for water, inside the channel they are 2. I define a box around the channel where the
membrane is and give it a dielectric of 2, and define a cylinder where the pore is in the
channel where i set the dielectric to 80.

I want to consider partial charges on the channel in the numerical solution of the
poisson boltzmann on the grid. I set up the routine as follows below. Do I need to have a
scalar charge command to include partial charges in the calculation or is it
automatically included?
Thanks very much!

stream radius.str
scalar wmain = radius sele all end
SOLVE nclx 71 ncly 71 nclz 91 dcel 1.0 -
XBcen 155.3 YBcen 155.3 ZBcen -48.5 maxit 500 -
epsw 80.0 conc 0.15 select all end -
epsp 2.0 -
Tmemb 34.0 Zmemb -48.0 epsm 2.0 Vmemb 0.0 -
Rcyln 7.0 Hcyln 34.0 epsc 80.0 Xcyln 155.3 Ycyln 155.3 Zcyln -48.0

open write card unit 16 name channel_close.dat
write phi volt card unit 16 xfirst 155.3 xlast 155.3 yfirst 155.3 ylast 155.3 -
zfirst -93.5 zlast -3.5
close unit 16 end