This is an example for calculating the membrane potential part of 
electrostatic energies for titration calculations at bR in a 
3-layer membrane environment.

kcsa.pqr       whole protein used for computing the ion accessible volume
               and calculating the interaction energy of the whole protein
	       with the membrane potential should consist of QM+MM region

cav.pqr        dummy atoms describing the cavities within the protein

dielectric regions:

the structures serve only for definition of the dielectric boundaries the
charges are not used

qm_region.pqr  placeholder since we have no QM region in the example,
               a quantum chemically or otherwise specially treated site
	       could be added here (e.g. the retinal), a different 
	       dielectric constant than in the rest of the protein can 
	       be used (normaly 1 for a QM region)

mm_region.pqr  the normal not quantum-chemically treated part of 
               the molecule, in this case identical to the whole structure

other files

channel.fpt   coordinates along the channel axis at which the potential
              is computed (identical to the points in the CHARMM calculation)

x.ogm         grid definition as usual

