Insight II |

Theory

Ideally, a user would like to graphically move the interacting molecules in real time on a workstation while computing the interaction energy. While the energy expression is straightforward to compute, the computation time increases as a square of the number of interacting atoms, making the process too slow for many molecular systems on most workstations.

As proposed by Langridge (Pattabiraman et al. 1985) an energy grid approximating the larger of the two molecules can be precomputed. Since the interaction energy can now be approximated by calculating the energy between the atom of the moving molecule and the appropriate grid points, the docking can be done in real time.

The construction of energy grids depends on the forcefield in use. This is explained in the following sections.

The interaction energy is now expressed as:

By using the position of the atom in the moving molecule to look up the value at the appropriate grid point, the interaction energy can be quickly computed.

It should be noted that as the grid spacing is decreased, the result of Eq. 8-8 becomes closer to the result of Eq. 8-7 since the error between the true atom position and the grid point decreases.

With the approximation of Eq. 8-14, the interaction energy can also be evaluated by Eq. 8-8 for CVFF.

Implementation

The **Evaluate** pulldown provides facilities for calculating the interaction energy between two molecules using explicit van der Waals energy (Eq. 8-9 or Eq. 8-7), explicit electrostatic (Coulombic) energy (Eq. 8-13), or the combination of van der Waals and electrostatic energies (Eq. 8-14). Alternatively, an energy grid can be used to calculate the interaction energy between two molecules (Eq. 8-7).

The **Grid **pulldown provides facilities for defining and calculating a potential energy grid which can be used for the evaluation of intermolecular energies. The overall size of the grid as well as the spacing between grid points can be specified.

Command Summary

Refer to the **Ampac/Mopac** Module chapter for summaries of the commands included in this pulldown.

An energy grid can be used to approximate intermolecular energy of very large systems. This grid can be on either molecule but must be calculated before activating this command, using the **Create** **Docking_Grid** and **Compute** **Docking_Grid** commands.

Docking Tutorial

Then, from the **Open Tutorial** window, select **Insight II ****tutorials**, then the **Docking **module and choose from the list of available lessons:

You can access the Open Tutorial window at any time by clicking the Open File button in the lower left corner of the Pilot window.

For a more complete description of Pilot and its use, click the on-screen help button in the Pilot interface or refer to the Insight II User Guide.