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4.1. Tripos MOL2 Format

This format is used for general molecule input and output of DOCK. Although previous versions of DOCK supported an extended PDB format to store molecule information, the current version now uses MOL2 as the molecule format. This format has the advantage of storing all the necessary information for atom features, position, and connectivity. It is also a standardized format that other modeling programs can read. For more information on how to generate MOL2 files from PDB files, go to the Structure Preparation demo.

Of the many record types in a MOL2 file, DOCK recognizes the following: MOLECULE, ATOM, BOND, SUBSTRUCTURE and SET. In the MOLECULE record, DOCK utilizes information about the molecule name and number of atoms, bonds, substructures and sets. In the ATOM record DOCK utilizes information about the atom names, types, coordinates, and partial charges. In the BOND record, DOCK utilizes the atom identifiers for the bond. In the SUBSTRUCTURE record, DOCK records the fields, but does not utilize them. The SET records are entirely optional. They are used only in special circumstances, like when ligand flexibility is considered. In DOCK 6, an additional record type has been introduced. This is the SOLVATION record, that has the atomic desolvation information for the ligand atoms. The parameter read_mol_solvation can be used to read in this record.

For extensive details on the MOL2 format, as well as example files, please refer to the Tripos web site documentation (

A 'multimol2' file is simply a bunch of mol2 files for the same ligand but different conformations that have been appended to each other. No other formatting is necessary.