AUTHOR: Brian K. Shoichet
The solvmap program calculates the grid that is used by DOCK6 for calculating ligand desolvation. Ligand desolvation is calculated as a sum of the atomic desolvation multiplied by a normalization factor that accounts for the extent to which the ligand atom is buried by the binding site. The atomic desolvation for each ligand atom can be calculated by AMSOL (AMSOL is not distributed by us, please follow the link for more information) and is stored in the input file (see file formats). 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. Thus the volume based ligand desolvation energy is calculated as:
Here L is the ligand atom desolvation, volume summed over k volume elements, V. This method is only an approximation to GB solvation and works within the limits of complete burial from the solvent and complete exposure to the solvent on the protein surface. However, being grid-based it is fast and can be used during conformational search and final scoring.
This programs require that an INSOLV file be created in the working directory, which contains the parameters to control the program. The INSOLV parameters for chemgrid are detailed below:
receptor.pdb; receptor file solvmap ; output grid file 1.4,1.3,1.7,2.2,2.2,1.8 ; radii of oxygen, nitrogen, carbon, sulfur, phosphorus, and "other" atoms. 1.4 ; radius of probe 1 ; grid resolution box.pdb ; box file
* OUTSOLV #restatement of input parameters; messages pertaining to calculation of the grids * solvmap #ligand desolvation grids