Mk_prepare_ligand fails for Vanadium-containing ligands

[frgoe003]

I noticed that the ligand preparation pipeline seems to fail for vanadium-containing ligands. Seems to be an issue with charge assignment:

..
atom number 23 has non finite charge, mol name: 1.B, charge: nan
atom number 24 has non finite charge, mol name: 1.B, charge: nan
atom number 25 has non finite charge, mol name: 1.B, charge: inf
..

Raised from meeko/writer.py

Code to reproduce:
mk_prepare_ligand.py -i AD9.sdf -o AD9.pdbqt

Examples:
AD9 from PDB 3MJX
-> AD9.sdf.zip

AOV from PDB 4AE3

[rwxayheee]

Hi @frgoe003
I have a PR pending review: #273. It provides the charge method to support the complicated chemical group involving metals. Please give it a try.

It takes two steps:
(1) Please check out my branch from PR #273 (equivalently this branch) and install with pip install -e ..

(2) Even with the charging method, it's required to manually put in the additional atom types. In your local branch, please edit this file: <directory to the downloaded repository>/Meeko/meeko/data/params/ad4_types.json
Add a new line anywhere, for example, after Mg:

    {"smarts": "[#12]",             "atype": "Mg"},
    {"smarts": "[#23]",             "atype": "V"},

To declare a unique autodock atom type for generic V atoms.

Now, you can run the command:
mk_prepare_ligand.py -i AD9.sdf

My output is:
AD9.pdbqt.txt

We would like to know your feedback and suggestions in handling these ligands. Please let us know what you think and if you have any further questions.