The conversion scheme described here was developed to be easy to use and accurate in its atom-typing and partial charge computation. Although still an area of active development, it has to date been been tested visually on several thousand compounds. Because of its ease of use and robustness, this route or a derivative thereof will likely be supplanting the dbprocess scheme which has been used in the past (here at UCSF, anyway). We provide you with both versions so that you may choose the method that suits you, and for backward compatibility.

This scheme consists of two programs run sequentially, one written in Fortran (sdf2mol2) and the other (sybdb) in Sybyl's programming language, SPL. Taken together, one can convert an MDL SDF-format database into a SYBYL MOL2 format database which has appropriate Sybyl atom types assigned, hydrogens added, and partial charges computed. To find out more about the conversion process, including how to use it, please consult the 00README file in the directory ./source/database/sdf2mol2 under the DOCK root.

Note: The second phase conversion requires Tripos' SYBYL for hydrogen addition and charge computation. The former program, sdf2mol2, may still be of some use to users who do not have SYBYL but have molecular modeling packages than can read MOL2 format (e.g. Biosym's Insight). Hydrogen addition, substructure removal, and charge computation must then be performed within the context of your own modeling package.