CalcPot

CalcPot - calculate electrostatic potential

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

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 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

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