MakeTNT-toolkit User Documentation | previous next |
MOL22TNT |
Copyright © 2004-2008 Global Phasing Limited
All rights reserved.
This software is proprietary to and embodies the
Author: (2004-2008) M. Brandl
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% MOL22TNT -i <input-file> [-n <tag>]\ [-o <filename>] [-FLEXTOR] [-noB] \ [-size <length of output>][-TightRestraints]\ [-ccp4][-ccp4_tnt][-Odict <O-database>][-notor][-OnoH][-HPDB] |
Switch | Argument | Description | Possible Values | Compulsory | Note | ||||||||||
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-i | <mol2-file> | name of mol2-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! |
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-o | <filename> | unique filename for TNT-dictionaries | e.g.: kinase_inhibitor986B, ... | no |
default = 3-letter code defined by -outname Choose something unique! |
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-FLEXTOR | output of default parameters for non-planar torsion angles | no | |||||||||||||
-noB | flag to suppress the output of default BCORREL restraints | no | |||||||||||||
-size | <length-of-output> | defines the overall size of the resulting dictionary |
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no |
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-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 | ||||||||||||
-HPDB | request of PDB-file including hydrogen positions of original MOL2-file | no | |||||||||||||
-TightRestraints | sigma for bond lengths: 0.020Å, sigma for bond angles: 2.0deg | no | default: 0.040Å, 5.0deg |
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:
Overlapping planes will result in one single TNT-PLANE restraint.
Planar 5/6-membered rings result in one PLANE restraint each. Recommended for large planar systems and in structures of high resolution.
Each planar torsion angle will result in a separate PLANE restraint.
Please note that TXL.mol2 has too many atoms/residue for O processing.
% MOL22TNT -i mdl189978.mol2 -n LIG -o ligand |
% MOL22TNT -i mdl189978.mol2 -n LIG -o ligand -CCP4 |
% MOL22TNT -i mdl189978.mol2 -n LIG -Odict -ODB stereo_chem.odb |
% MOL22TNT -i mdl189978.mol2 -n LIG -Odict -ODB stereo_chem.odb -notor |
if you do not wish to restrain flexible torsions
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, Global Phasing) 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).