Solvgrid

3.2.3 SOLVGRID

AUTHOR Kaushik Raha

DESCRIPTION:

The solvgrid program creates bulk (or receptor) and explicit (or ligand) desolvation grids using the occupancy desolvation method (Luty et. al., J. Comp. Chem, 1995; Verkhiver et. al., J. Mol. Recog., 1999). The occupancy desolvation method is phenomenonlogical in nature where desolvation energy can be described pairwise additively. The desolvation energy due to interaction between a ligand atom and receptor atom can be calculated as the solvent affinity of a ligand atom weighted by the volume of the solvent displaced from the receptor atom due to binding and vice versa. Thus,

                                               Edsol  =  Si øDES,EXPL(xi) +  fi øDES,BULK(xi)

Where the mobile atom i, has a solvation affinity of Si and a fragmental volume of fi. The solvent affinity of the ligand atom is calculated as:

                                                 lig_atm_sol

Where qi is the charge on the ligand atom i, and alpha and beta are constants set at alpha = 0.25 kcal/mol and beta = -0.005 kcal/mol. fi is the volume of ligand atom i, calculated from the amber radius of the ligand atom. For the receptor, these can be precalculated and stored on a grid. øDES,BULK(xi) and øDES,EXPL(xi) are interpolated from grids calculated using the solvgrid program during docking. It requires the calculation of two separate grids:

                                           blk_exp_dsol_grd

where j is a rigid receptor atom, and Sj and fj are the solvent affinity and the fragmental volume of the receptor atom respectively. Bulk and explicit desolvation grids are calculated from fj and Sj at grid points p, distance rjp from the receptor atom multiplied by gaussian weighting of the distance. The solvgrid program calculates these grids from the charge and the volume of the receptor atoms.

USAGE: solvgrid

INPUT

This programs require that an INRDSL file be created in the working directory, which contains the parameters to control the program. The INRDSL parameters for solvgrid are detailed below:

   receptor.pdb ; receptor pdb file
   parameters/ prot.table.ambcrg.ambH ; charge parameter file
   parameters/ vdw.parms.amb.mindock ; VDW parameter file
   box.pdb ; box pdb file
   0.33 ; grid spacing in angstroms
   1 ; es type: distance-dependent dielectric; 2: constant dielectric
   4 ; es scale for ff scoring
   2.3 2.8 ; bumping distances for polar and non-polar receptor atoms
   output_prefix ; output grid prefix name
   sol_op ; method for calculating desolvation grid
   solE_recep; solvation free energy of receptor

OUTPUT FILES

   * OUTRDSL #restatement of input parameters; messages pertaining to calculation of the grids
   * OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file
   * PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file
   * output_prefix.bmp #bump grid
   * output_prefix.vdw #vdw values for receptor
   * output_prefix.es #electrostatic values for receptor
   * output_prefix.dsl #bulk and explicit desolvation grid for receptor