The article describes PRODRG, a tool for generating high-throughput crystallography data for protein-ligand complexes. PRODRG automatically generates coordinates and molecular topologies suitable for X-ray refinement from various input formats, including existing coordinates or two-dimensional representations. It is tested against the Cambridge Structural Database (CSD) and a number of protein-ligand complexes. The program is capable of generating topologies for use with a wide range of software, including crystallographic refinement programs and docking programs. PRODRG is tested against the CSD and shows that it can generate structures with good geometries within the limits of the empirical GROMOS87 force field. X-ray refinement using PRODRG-generated topologies produces results comparable to those using standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better in terms of ligand geometry and crystallographic R factors. PRODRG is also compared with similar programs such as XPLO2D and REFMAC5/LIBCHECK. It is found that PRODRG-generated topologies perform well in crystallographic refinement. The program is limited in the scope of compounds it can handle due to its dependence on the GROMOS87 force field and the limited number of atom types it supports. The article concludes that PRODRG provides fast, automated, and reliable access to small-molecule topologies and coordinates for use in high-throughput protein-ligand crystallography. It is also noted that further improvements are being developed to overcome the limitations in terms of atom types and force fields.The article describes PRODRG, a tool for generating high-throughput crystallography data for protein-ligand complexes. PRODRG automatically generates coordinates and molecular topologies suitable for X-ray refinement from various input formats, including existing coordinates or two-dimensional representations. It is tested against the Cambridge Structural Database (CSD) and a number of protein-ligand complexes. The program is capable of generating topologies for use with a wide range of software, including crystallographic refinement programs and docking programs. PRODRG is tested against the CSD and shows that it can generate structures with good geometries within the limits of the empirical GROMOS87 force field. X-ray refinement using PRODRG-generated topologies produces results comparable to those using standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better in terms of ligand geometry and crystallographic R factors. PRODRG is also compared with similar programs such as XPLO2D and REFMAC5/LIBCHECK. It is found that PRODRG-generated topologies perform well in crystallographic refinement. The program is limited in the scope of compounds it can handle due to its dependence on the GROMOS87 force field and the limited number of atom types it supports. The article concludes that PRODRG provides fast, automated, and reliable access to small-molecule topologies and coordinates for use in high-throughput protein-ligand crystallography. It is also noted that further improvements are being developed to overcome the limitations in terms of atom types and force fields.