7.8 Evaluation of the interactions | ![]() |
In order to analyze the docking results, VEGA can
calculate the interaction energy ligand - biomacromolecule and evaluate the contribute of
each residue. This function is available choosing Claculate -> Interactions
from the main menu.
For the calculation, you must indicate the ligand typing the residue name and the residue
number in the Ligand/residue field (format : Residue_Name:Residue_Number).
It's possible to put also the lone residue number or to click on the lignad structure in
the main windows to select the ligand.
The Dielectric (dielectric constant) and the Cutoff (cutoff
distance) parameters are strictly related to the evaluation of the non-bond interaction
energy. VEGA applies the CVFF force field parametrization using the R6-R12
Lennard-Johnes' and the Coulomb's equations. Only the residues in which the energetic
contribute is over the Trashold (%), are showed in the table and in the graphic
main window.
You can modify the visualization choosing the coloring method (Ligand by atom, By molecue and By residue) and which residues to show (Ligand, receptor Residues and Water molecules).
An output example is the following:
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Red = receptor residues Green = ligand |
In the console you can find all numerical data:
********************************************* **** CVFF interaction energy calculation **** ********************************************* Ligand name..........: DES_9999 Ligand atoms.........: 75 Dielectric constant..: 20.000 Total................: -51.6411 Kcal/mol Non-bond.............: -34.3118 Kcal/mol Coulombic............: -17.3293 Kcal/mol Res Num R6-R12 Coulomb Total % ===================================================== LYS 110 -5.7706 -1.7536 -7.5243 14.57 ZN 732 -0.2007 -6.6566 -6.8574 13.28 HIS 542 -3.0452 -1.0418 -4.0870 7.91 ARG 585 -0.9352 -2.8797 -3.8150 7.39 LYS 588 -0.6616 -2.7608 -3.4224 6.63 HIS 147 -3.0544 -0.0717 -3.1262 6.05 TYR 655 -3.1364 0.0201 -3.1163 6.03 TYR 594 -2.7546 -0.0895 -2.8441 5.51