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Creating a New Ligand Type

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Victoria Ingman edited this page Aug 3, 2018 · 3 revisions

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Overview

AaronTools has a limited number of ligands included in a built-in Ligand Library. If you wish to screen custom ligands these can be easily added to your Personal Aaron Library.

Adding Ligands to $HOME/AARON_libs/Ligands

AaronTools comes with a simple utility (libadd_ligand) that will extract the ligand from a provided XYZ file and add it to your personal ligand library ($HOME/Aaron_libs/Ligands).

Note: libadd_ligand relies on your XYZ file following the AaronTools convention: substrate atoms, then transition metal center, then ligand. It is a good idea to check the geometry of the new ligand in your personal library before you use it!

To add a new ligand:

  1. Start with an XYZ file containing your ligand bound to a metal and at least one other non-metal atom (file.xyz)
  2. Re-order the atoms such that the ligand occurs after the metal, which occurs after at least one non-ligand atom
  3. Run
 libadd_ligand file.xyz -n NAME

This will extract the ligand from file.xyz and add the properly formatted file to 

 $HOME/Aaron_libs/Ligands/NAME.xyz

Once you have added new ligand(s) to $HOME/AARON_libs/Ligands, you can specify these in an AARON input file or in map_ligand as you would with any of the built-in ligands: 

 map_ligand catalyst.xyz -l NAME

Note: Currently, AaronTools does not support ligands that contain metals (e.g. DPPF).

Format for Ligand XYZ files

Ligand files are standard XYZ files with additional information provided in the comment line.

For ligands that will bind metals, the ligand should be positioned such that the transition metal would be at the origin. The only information required on the comment line is a list of atoms that bind the metal. These are specified by 'K:' followed by a comma-separated list of atom numbers: 

 #atoms
 K:atom1,atom2;
 [coordinates]

For example, the following XYZ specifies the DHPE ligand, where the phosphorous that bind the metal are atoms 1 and 4: 

 12
 K:1,4
 P      -1.755101      0.143572      1.288922
 H      -2.806723     -0.652562      1.001237
 H      -2.226461      1.407144      1.349787
 P       1.752826     -0.145957      1.291747
 H       2.804952      0.650705      1.007389
 H       2.224080     -1.409641      1.351107
 C       0.739170      0.369668      2.817318
 C      -0.744135     -0.374874      2.815323
 H      -1.301886     -0.138137      3.697235
 H      -0.560468     -1.428296      2.777011
 H       0.555569      1.423160      2.780630
 H       1.295365      0.131300      3.699774

Ligand Naming

By default, AaronTools will search for ligands in the following order: 

 $HOME/Aaron_libs/Ligands
 $QCHASM/AaronTools/Ligands

So, if you create a new ligand with the same name as one in the built-in AaronTools ligand library, your new ligand will be used rather than the built-in one.

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