MakeTNT-toolkit User Documentation previous next


Copyright © 2004-2008 Global Phasing Limited

All rights reserved.

This software is proprietary to and embodies the
confidential technology of Global Phasing Limited (GPhL).
Possession, use, duplication or dissemination of the software is
authorised only pursuant to a valid written licence from GPhL.

Author: (2004-2008) M. Brandl


General Information

MOL22TNT is a Java-based command line tool to generate TNT-restraints from a Tripos *.mol2 file.

Command Line Switches and Arguments

Conversion Mechanism:

Restraint atoms are selected on the basis of a molecular graph generated from the bond-list of the mol2-file. Target values for restraints are taken from the 3D-coordinates. If present the positions of H-atoms are used to improve the quality of the restraints. As Buster-TNT presently does not support the refinement of hydrogen atoms, they are removed from the final restraint file.

If an atom has three neighbours bonded to it, an improper torsion is measured between those four atoms and if its value is close to 0 or 180 degrees (tolerance: 10 degrees), a TRIGONAL restraint is generated, otherwise an IMPROPER torsion restraint is generated. IMPROPER torsion restraints are also generated for atoms surrounded by four (or more) neighbours.

A PLANE restraint is formed around bonds:

The different options for the -size argument are:


Using MDL2TNT in its default mode, the following output files are written into the working directory: With the -CCP4 flag, two files are generated: If you choose the -Odict option, you will obtain: If you choose -Odict, -ODB <O-database>:


Example input files (mdl189978.mol2, TXL.mol2) can be found in: samples/maketnt/MOL22TNT.

Please note that TXL.mol2 has too many atoms/residue for O processing.


Derivation of TNT-dictionary restraints from *mol2 files has been tested on a data set of 1000 compounds from the NCI-database Dictionaries from 20 *mol2 files (NSC-Numbers: 325, 333, 334, 335, 396, 400, 408, 463, 479, 533, 551, 556, 558, 604, 741, 790, 811, 870, 871, 872) have been checked for their performance in re-optimizing (Gelly, O.Smart, Globalphasing) a corresponding PDB-file (generated by Corina) after an initial distortion to an RMSD-value of 0.25A. Manual inspection showed consistent optimization for all 20 test-cases (data available on request).

Maria Brandl,<>
Last modification: 02.02.07