Ligand desolvation is calculated as a part of the dock3.5 score as implemented in DOCK 6. There are two options to calculate ligand desolvation: full and volume based. Atomic desolvation for each atom in the ligand is calculated using AMSOL. Full desolvation is calculated as a sum over atomic desolvation. Volume based desolvation is calculated by multiplying the atomic desolvation by a normalization factor that accounts for the burial of the ligand atom in the binding site. The cost of desolvating each atom, or the normalization factor, is the distance weighted high dielectric volume displaced by the protein that is stored for each grid element in the active site. This calculated by the program solvmap distributed with DOCK 6. For more information please see the DOCK6 manual.
Creating SOLVMAP grids
To create a SOLVMAP you will need:
- Input instructions in a local INSOLV file
- Example in $DOCK6_HOME/install/test/solvgrid_generation/INSOLV
- Your protein/receptor in PDB format.
- Example in $DOCK6_HOME/install/test/solvgrid_generation/rec.crg
- Bounding box for the grid
- Example in $DOCK6_HOME/install/test/solvgrid_generation/box
The phimap can then be created by running the executable solvmap in $DOCK6_HOME/bin as:
where $DOCK6_HOME refers to the your DOCK6 distribution.