1. Introduction

GriDock was designed to perform the molecular dockings of a large number of ligands stored in a single database (in a format supported by VEGA) in the lowest possible time. It take the full advantage of all local and remote CPUs thanks the MPICH2 technology, balancing the computational load between processors/grid nodes. The docking procedure consists in some steps:

1. Extraction of the molecule from the database (VEGA command line).
2. Addition of the hydrogens if they are missing (VEGA command line).
3. Atomic charges calculation, potential attribution (AMBER), search of the flexible torsion angles and conversion in PDBQT format (VEGA command line).
4. Molecular docking (AutoDock 4).
5. Selection of the best scored complex and ranking in the result list.
6. Storing of the AutoDock output in a compressed Zip archive for a successive analysis (e.g. with VEGA ZZ 2.3.0).

Main features:

• No database pre-processing needed. The ligands can be stored in 2D or 3D with or without hydrogens.
• No external scripts. GriDock is a monolithic softtware written in C++ and it's based on the VegaLib runtime.
• Easy to use even if it's a command line-based software. It requires two parameters only to run: the receptor file name and the ligand database.
• Windows executable for both thread an MPICH2 versions.
  Linux 32 and 64 bit executables for both pthread and MPICH2 versions.