Module: Noncovalent Interaction Grid ()

Description:

This module generates a grid which contains the noncovalent interaction energy between the input molecule and a probe atom at each grid point. The energy will be computed with the MMFF94 forcefield in kJ/mol. Grid dimensions and atom parameters for the probe atoms can be chosen by the user. The molecule must have MMFF94 parameters assigned. You can add parameters by using the 'Add MMFF Parameterization' menu entry in the MoleculeEdior or with the addMMFFParameterization tcl command of the molecule.

Connections:

Data [required]
The molecule for which the interaction energy will be computed.

Ports:

Atom Type

Allows the user to select the MMFF atom type of the probe atom. This atom type determines all van der Waals Parameters.

Atom Charge

For the MMFF94 forcefield the charge of the atom is a function of the atoms formal charge and surrounding atoms by adjusting the charge according to bond charge increments. The probe atom has no bonds so the charge value needs to be adjusted by the user. Whenever the user choses a new atom type, the value will be set to its formal charge. This parameter has no effect if the Coulomb energy is deactivated.

Energy

Sets which noncovalent energy components are computed.

Sampling Options

Lattice Box

Allows the user to adjust the bounding box of the grid.

Voxel size

Allows the user to adjust the voxel size of the grid

Dimensions

Shows the dimensions of the field. Large fields will take a long time to compute and computation may fail due to insufficient memory.