Chemgrid

From DISI
Jump to: navigation, search

3.2.1. CHEMGRID

AUTHOR: Brian K. Shoichet

DESCRIPTION:

This program chemgrid produces values for computing force field scores and bump checking. The force field scores, or molecular mechanics interaction energies are calculated as van der Waals and electrostatic components and stored on grids. The calculations are based on the theory presented in the Grid section above. However only the steric interaction energy grids are used in DOCK 6 as a part of Dock3.5 Score. The electrostatic interaction calculation differs from Energy Scoring in the following aspects. For calculating the electrostatic interaction, the electrostatic potential of the receptor calculated using the linearized form of Poisson-Boltzmann equation:

npbe_score_eqn

Where phi(x) the potential is determined by the dielectric function epsilon(x), a modified Debye-Huckel parameter kappa(x), and the charge density of the receptor rho(x). The electrostatic potential map (or phimap) is calculated using DelPhi and then is used by DOCK 6 to calculate the electrostatic interaction energy as: delphi_elec_score Where, qi the partial charge of every atom i, is multiplied by the electrostatic potential of the receptor phi at the respective atomic position. Trilinear interpolation method is used for interpolating the electrostatic potential from the phimap on to the ligand position.

USAGE: chemgrid

INPUT FILE:

This programs require that an INCHEM file be created in the working directory, which contains the parameters to control the program. The INCHEM parameters for chemgrid 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
   1 ; es scale for ff scoring
   2.3 2.8 ; bumping distances for polar and non-polar receptor atoms
   output_prefix ; output grid prefix name

OUTPUT FILES

   * OUTCHEM #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