Method=<type name>

To tell which method type to use, type name can be MC or BS (Bestsite) (the default value)

testonly=<bool>

To compute minimal and maximal voltage among the ion accessible grid points for test only (no ion to put in) if the value is true. It's valid only for BS method.

ion=<string>

To tell the residue type of ion to be added

GridSize=<real>

To tell the grid size for building ion accessible gridding points

Crdfile=<file name>

To tell a ion structure file for a complex ion

Crdfmt=<type name>

To tell the format of crdfile fed in, current Modar supports PDB or Charmm format structure file.

Radius=<real>

To tell the VdW radius of the ion to be added, Modar can retrieve the radius value from the force field automatically. However, for a complex ion, it’s better to tell the radius value manually.

rExt=<real>

Extra extended probe radius value for building ion accessible grid points

Iseed=<int>

To assign the initial seed for random number generator which is needed for MC method

nMC=<int>

Number of Monte Carle move cycle for MC method

Vmin

The minimal voltage value among all the ion accessible grid points

Vmax

The maximal voltage value among all the ion accessible grid points

Vavg

The average voltage over all ion accessible grid points

Vsig

The standard deviation voltage over all ion accessible grid points