MakeTNT-toolkit User Documentation	previous next
MDL2TNT

MDL2TNT

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
Command Line Switches and Arguments
Conversion Mechanism
Output
Examples

General Information

MDL2TNT is a Java-based command line tool to generate TNT-restraints from a 3D-MDL-file.

Command Line Switches and Arguments

Usage of MDL2TNT:

% MDL2TNT -i <input-file> [-n <tag>] \ [-o <filename>] [-FLEXTOR] [-noB] \ [-size <length of output>] [-normBO][-HPOS][-ccp4][-ccp4_tnt][-Odict]\ [-Odict][-ODB <O-database>][-OnoH][-notor][-TightRestraints]

Switch Argument Description Possible Values Compulsory Note

-i <mdl-file> name of MDL-file submitted no format restrictions, any extension yes

-n <tag> <3-Letter code to be used in TNT-dictionary file> e.g.: ATP,GMP,ANY,THI,NGY,OUL,IKE no default = UNK
Use your own!

-o <filename> unique filename for TNT-dictionaries e.g.: kinase_inhibitor986B, ... no default = 3-letter code defined by -outname
Choose something unique!

-noB flag to suppress BCORREL restraints no

-FLEXTOR output of default parameters for non-planar torsion angles no

-size <length-of-output> defines the overall size of the resulting dictionary

s (short)

m (medium)

l (long)

no

default : s (small)

see also : Conversion Mechanism

-HPOS Switch to ignore H-atom positions no Not recommended ! Use only if H-atoms are unreliable

-normBO Assume normalised bond orders no Recommended if your file has normalised bond orders

-ccp4 flag to generate CCP4-restraints instead of TNT-restraints no

-ccp4_tnt flag to generate CCP4-restraints AND TNT-restraints no

-Odict flag to generate dictionaries for O instead of TNT-restraints no

-ODB <O-database> append non-redundant O-dicionaries to existing O-database no only relevant to the generation of O-dictionaries

-OnoH exclude hydrogen atoms from O-dictionary entries no only relevant to the generation of O-dictionaries

-notor flag to suppress torsion restraints for non-planar groups in O-dictionaries no only relevant in combination with -Odict

-TightRestraints sigma for bond lengths: 0.020Å, sigma for bond angles: 2.0deg no default: 0.040Å, 5.0deg

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:

s (small, default):
Overlapping planes will result in one single TNT-PLANE restraint.
m (medium):
Planar 5/6-membered rings result in one PLANE restraint each. Recommended for large planar systems and in structures of high resolution.
l (long):
Each planar torsion angle will result in a separate PLANE restraint.

Output:

Using MDL2TNT in its default mode, the following output files are written into the working directory:

TNT-dictionary file: <filename>.dic (e.g. ligand.dic)

PDB-file without H-pos for refinement: <tag>.pdb (e.g. LIG_tnt.pdb)

if -HPDB is set: PDB-file including original H-pos for refinement: <tag>.pdb (e.g. LIG_H_tnt.pdb)

With the -CCP4 flag, two files are generated:

dictionary file for Refmac (e.g: ligand.GPhL.cif)

PDB-file (with H-pos): LIG_tnt.pdb

If you choose the -Odict option, you will obtain:

dictionary file: e.g.: ligand_O_refi_dict.txt
dictionary header-file: ligand_O_refi_dict.hd (.bond_angles count line)
PDB-file: LIG_tnt.pdb

If you choose -Odict, -ODB <O-database>

the new dictionary will be appended to the existing O-database

if the database does not yet include an entry for a residue of the 3-letter code specified

Example:

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.

To produce a TNT-dictionary file for mdl824.mol, please run:

% MDL2TNT -i mdl824.mol -n LIG -o ligand

For Refmac-restraints, run:

% MDL2TNT -i mdl824.mol -n LIG -o ligand -CCP4

To add an entry to the O-library:

% MDL2TNT -i mdl824.mol -n LIG -Odict -ODB stereo_chem.odb
or

% MDL2TNT -i mdl824.mol -n LIG -Odict -ODB stereo_chem.odb -notor

if you do not wish to restrain flexible torsions

Maria Brandl,<buster-develop@GlobalPhasing.com>