NAME
     CalcPot - calculate electrostatic potential

SYNOPSIS
     CalcPot expr expr expr expr expr expr
         expr ( zero | debye ) fileName

DESCRIPTION
     Calculate the electrostatic potential of all
     selected molecules, and write the result to a
     file with the given name. The resolution (grid
     density) depends on DrawPrec.

     The first argument is the radius of the atoms, you
     will normally not change the default value 'vdw'.

     The second argument determines the charge of the
     atoms, typical values are:

         charge: partial charges on all atoms

         heavycharge: partial charges of protons
             transferred to heavy atoms

         avgcharge: partial charges on heavy atoms,
             averaged over neighbours

         simplecharge: charges only on one or two atoms
             of charged residues, as specified in the
             setup file AtomCharges

     The third argument gives the dielectricity constant
     for the molecule, typically in the range 2 to 4, the
     fourth for the solvent, normally 80.

     The fifth argument gives the solvent radius,
     normally 1.4 for water.

     The sixth argument gives the salt concentration as
     ionic strength. For simple salts, this is twice the
     concentration, so the default value of 0.3
     corresponds to a salt concentration of 150 mMol.

     The seventh argument gives the salt radius.

     The eighth argument gives the size in Angstroms
     that (on each side) the box that the potential is
     calculated in is larger than the extent of the
     molecule. Values of 10 to 15 are recommended.
     Smaller values reduce the calculation time, but may
     introduce artifacts from the boundary conditions.

     The ninth argument selects the kind of boundary
     condition, either values fixed at zero, or
     Debye-Hueckel. Using zero is faster, and there
     does not seem to be a noticable difference between
     the two.

     For correct results, special care should be taken
     that the residue definitions with the correct
     charges are used. This is expecially important when
     using PDB files, because the residue names in there
     normally do not contain the charges. There is a
     standard macro called pdb_charge.mac that can be
     run after reading PDB files, it should normally do
     the necessary corrections. For the N and C termini,
     the molecules should have charged end groups, or
     special forms of the residues that contain the
     necessary charges.

     Depending on the precision, this function can use
     a lot of memory, an error message will be given
     if the memory runs out.

     This command supports groups.

EXAMPLE
     CalcPot vdw charge 2.0 80.0 1.4 0.3 2.0
	 10.0 zero foo.pot

REFERENCE
     Nicholls, A, Honig, B.
     A rapid finite difference algorithm, utilizing
     successive over-relaxation to solve the
     Poisson-Bolzmann equation.
     Journal of Computational Chemistry, 12 (1990) 435-445

SEE ALSO
     SelectMol, SelectAtom, DrawPrec, Group, PathNames,
     AddSurface, ReadPot, PaintSurface

DATE
     960621
