Delphi electrostatics

The 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. However only the steric interaction energy grids are used in DOCK 6 as a part of Dock3.5 Score. For calculating the electrostatic interaction, the electrostatic potential of the receptor calculated using the linearized form of Poisson-Boltzmann equation. And electrostatic interaction energy between the ligand and the receptor is calculated from this grid. For more information please see the DOCK6 manual.

Creating DelPhi electrostatic grids

To create a DelPhi electrostatic grid (phimap) you will need:

1. The DelPhi program
2. Your protein/receptor in PDB format with delphi spheres added.
   • Example in $DOCK6_HOME/install/test/chemgrid_generation/rec+sph.crg
3. Atomic charges
   • Example in $DOCK6_HOME/install/test/chemgrid_generation/amb.crg.oxt
4. Atomic radii
   • Example in $DOCK6_HOME/install/test/chemgrid_generation/vdw.siz
5. Parameters for running the calculation
   • Example in $DOCK6_HOME/install/test/chemgrid_generation/generic.prm

The phimap can then be created by running the script make_phimap in $DOCK6_HOME/bin as:

 $DOCK6_HOME/bin/make_phimap $DELPHI_PATH

$DOCK6_HOME refers to the your DOCK6 distribution and $DELPHI_PATH refers is the path of your DelPhi distribution

Visualizing DelPhi grids

Visualizing_delphi

--Kaushik 09:08, 15 October 2006 (PDT)