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