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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

MDL2TNT is a Java-based command line tool to generate TNT-restraints from a 3D-MDL-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 MDL-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 (this can be suppressed by the -HPOS option). 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 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.

Recognition of planar torsion restraints is mainly based on connectivity information, yet needs to be confirmed by an approximately planar constellation in the 3D-coordinates. If connectivity and coordinate information contradict each other (e.g. steric hindrances in large conjugated systems), restraints are not formed and a message to the user is written instead. Planarity recognition works best, if bond orders in your input file are normalised and you specify -normBO as an input flag.

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 (mdl824.mol, TXL.mol) can be found in: samples/maketnt/MDL2TNT.

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

Maria Brandl,<>
Last modification: 02.02.07