The GlycoBioChem PRODRG2 Server
PRODRG will take a description of a small molecule (as PDB coordinates / MDL Molfile / SYBYL Mol2 file / text drawing) and from it generate a variety of topologies for use with GROMACS, WHAT IF, Autodock, HEX, CNS, REFMAC5, SHELX, O and other programs, as well as energy-minimized coordinates in a variety of formats.
Please note that this server is strictly for academic use (max 5 submissions/day) only. For more extensive or commercial use you can obtain your own copy of PRODRG.
A list of some frequently asked questions is available is available, please have a look at it if you are having problems with PRODRG's output. If that does not help, or you have other comments/suggestions, feel free to email Daan van Aalten.
If you use the data generated by this server in a publication, please cite: A. W. Schüttelkopf and D. M. F. van Aalten (2004). PRODRG - a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D60, 1355–1363. [PMID 15272157, reprint avilable here]