MakeTNT

Contents

• General Information
• Command Line Switches and Arguments
• Conversion Mechanism
• Output
• Examples
• Evaluation

General Information

• generate REFMAC restraints instead of TNT-restraints
• convert TNT-restraints into Refmac-format

Command Line Switches and Arguments

• Usage of MakeTNT:

  % MakeTNT -source <program> \ -top <topology-file> -par <parameter-file> \ [-o <filename>] [-n <TNT tag>]  \ [-size <length of output>] [-noB] \ [-ccp4][-Odict][-ODB <O-database>][-PDBTOR <pdb-file>]

  The following table will show more details on how to

  • specify input files to MakeTNT
  • specify the name (3-letter code) of the ligand in the restraint geometry cards
  • specify the name of the output dictionary file
  TNT-geometry files generally have the extention ".dic"

  Switch	Argument	Description	Possible Values	Compulsory	Note
  -source	<program>	source of restraint information to be converted to TNT-format	XPLOR_CORINA, REFMAC, XPLOR_XPLO2D, TNT	yes
  -top	<topology-file>	file defining ligand topology	see: Example Section	yes :  XPLOR no :  REFMAC	see also: -source
  -par	<parameter-file>	file listing ligand restraints	see: Example Section	yes	see also: -source
  -n	<tag>	3-(capital)-letter residue name 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 -n Choose something unique!
  -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
  -noB		flag to suppress default BCORREL restraints		no
  -ccp4		flag to put Refmac - restraints instead of TNT-restraints		no
  -Odict		generate O-dictionaries 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
  -PDBTOR	PDB-file	derive value of planar torsions (0/180°) from PDB-file		no	only relevant to the generation of O-dictionaries
  -PDBREF	PDB-file	derive element symbols from PDB-file		no	only relevant to the conversion: TNT-dictionary -> *cif-dictionary for Coot

Conversion Mechanism:

• bond and angle restraints: --> BOND and ANGLE
• torsion restraints:
  • planar: --> PLANE (can be controlled by -size command line argument)
  • non-planar: ignored
• improper torsion restraints:
  • planar: --> TRIGONAL
  • non-planar: --> IMPROPER (order of atoms changed from CABD to ABCD)
• Libcheck/Refmac plane restraints: --> PLANE(independent of "-size" command line argument)

  Libcheck/Refmac uses definitions similar to s (small) and not a complete description like CORINA. In this case s and l options will result in a very similar output. Planar ring recognition (when using m) is not possible. Therefore, for size m a size l dictionary file is produced.

• Libcheck/Refmac "chiral volume" restraints:
  • if the Refmac dictionary-file includes xyz cartesian coordinates: --> IMPROPER calculated
  • direct conversion from chiral volumes can be added on request

• s (small):

  Overlapping planes will give one single TNT-PLANE restraint: this is recommended for visualisation.

• m (medium):

  Planar 5/6-membered rings give one PLANE restraint each (for Refmac input, size  l is generated instead).

• l (long):

  Restraints are generated as specified in input.

Output:

• TNT-dictionary file <filename>.dic (e.g. staurosporine.dic)
• for Libcheck/Refmac-input including coordinates: PDB-file

• CCP4-library file (e.g. LIG.GPhL.cif)

• dictionary file: e.g.: LIG_O_refi_dict.txt
• dictionary header-file: TXL_O_refi_dict.hd (.bond_angles count line)

• 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

• to specify planar torsions in O-dictionaries (0/180°).
• The PDB-file is only used to derive the direction of planar torsions. Everything else is derived from the restraint files.

Examples:

• CORINA:
  • run the command

    % MakeTNT -source XPLOR_CORINA  \ -top nsc628503.top -par nsc628503.par \ -n TXL -o taxotere

  • for atom numbers > 100 CORINA atom names consist of the chemical element only
    • for those atoms MakeTNT creates numbers based on two digits and 26-symbols (0+A-F,H-Z), each , e.g.

    100 = 00; 101 = 0A, 102 = 0B, 126 = A0, ... 
    

    • to label your PDB-file in the same way, please use MakePDB (a small additional application constructed for this purpose):

      % MakePDB -source PDB -input nsc628503.pdb

      In this example, H-atoms are included for demonstration purposes. At the moment, hydrogen atoms are not used during refinement with BUSTER-TNT and should be removed from the coordinate files.

• Libcheck/Refmac:
  • please check MakeTNT's current format requirements for Refmac restraint dictionaries
  • run the command

    % MakeTNT -source REFMAC \ -par ATP.lib \ -n ATP -o adenosinetriphosphate

• XPLOR:
  • run the command

    % MakeTNT -source XPLOR_XPLO2D \ -top brl_xplor_top.txt -par brl_xplor_par.txt \ -n BRL -size s -o rosiglitazone

• XPLOR to Refmac:
  • run the command

    % MakeTNT -source XPLOR_XPLO2D \ -top brl_xplor_top.txt -par brl_xplor_par.txt \ -n BRL -size s -o rosiglitazone  -ccp4

• TNT to CCP4:
  • go back to the CORINA-directory and run the command

    MakeTNT -source TNT -par taxotere.dic -ccp4 -n TXL -PDBREF TXL_tnt.pdb

• TNT to O
  • go back to the PDB2TNT-directory and create a local version of the O-library a

    cp $ODAT/stero_chem.odb .

    then run the command:

    MakeTNT -source TNT -par taxotere.dic -n TXL -Odict -ODB stereo_chem.odb

    In the above run, planar torsions for your dictionary have been read from the comments in taxotere.dic (NOTE - tag).

  • If your TNT-dictionary file does not have planar torsions included as comments (any TNT-dictionary file produced by MakeTNT, or by the other tools prior to version 1.9.2), you can specify a PDB-file which will be used to assign the directions of planar torsions, please use:

    MakeTNT -source TNT -par taxotere.dic -n TXL -Odict -ODB stereo_chem.odb -PDBTOR TXL_tnt.pdb

    If a PDB-file is submitted by -PDBTOR, commented planar torsions in the TNT-dictionary file will be ignored.

  • A few words of caution:
    • All input available to MakeTNT - tools can be converted into O-dictionaries, yet O has problems processing residues with more than 100 atoms (as in the H-atom including taxotere structures in this documentation)
    • Upon loading a PDB-structure, by default O would omit H-atom positions. O-dictionaries at the moment do include H-atom positions, thus hydrogens need to be included when loading a ligand into O.